Index (SeqWare 0.13.4 API)

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abisolid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
AbortLoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller: AbortLoadIndexPageController class.
AbortLoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController: Constructor for AbortLoadIndexPageController.
abortTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: abortTransaction.
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: abortTransaction.
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: abortTransaction.
abortTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: abortTransaction.
abortTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: abortTransaction.
AbstractInMemoryPlugin - Class in com.github.seqware.queryengine.plugins.inmemory: Base class for all in-memory plug-ins
AbstractInMemoryPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
AbstractInMemorySet<S extends MolSetInterface,T> - Class in com.github.seqware.queryengine.model.impl.inMemory: An in-memory representation of a MolSetInterface.
AbstractInMemorySet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet: Constructor for AbstractInMemorySet.
AbstractJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
AbstractJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: for bash Job
AbstractJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: for Java/Perl/JavaModule job
AbstractMolSet<S extends MolSetInterface> - Class in com.github.seqware.queryengine.model.impl: Implements TTL behaviour for sets
AbstractMolSet() - Constructor for class com.github.seqware.queryengine.model.impl.AbstractMolSet: Constructor for AbstractMolSet.
AbstractMRHBaseBatchedPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: This plug-in abstracts plug-ins that use a model manager to keep track of Features that "pass" the mapper
AbstractMRHBaseBatchedPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin
AbstractMRHBasePlugin<ReturnType> - Class in com.github.seqware.queryengine.plugins.hbasemr: Abstract implementation of an abstract map/reduce-based plug-in for a HBase back-end.
AbstractMRHBasePlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
AbstractMRInMemoryPlugin - Class in com.github.seqware.queryengine.plugins.inmemory: Base class for all in-memory plug-ins that do MR
AbstractMRInMemoryPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.AbstractMRInMemoryPlugin
AbstractScanInMemoryPlugin - Class in com.github.seqware.queryengine.plugins.inmemory: Base class for all in-memory plug-ins that do Scan
AbstractScanInMemoryPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.AbstractScanInMemoryPlugin
AbstractWorkflowDataModel - Class in net.sourceforge.seqware.pipeline.workflowV2
AbstractWorkflowDataModel() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
AbstractWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2
AbstractWorkflowEngine() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine
abundancemeasurement - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
accept(Representation) - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource: accept.
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
accession - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
ACCESSION_ONLY - Static variable in class com.github.seqware.queryengine.system.importers.OBOImporter: Determines whether we use "acccession-only" tags.
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
accessKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
ACL - Class in com.github.seqware.queryengine.model.interfaces: Access control list that determines permissions and access rights to features and feature sets.
ACL.Builder - Class in com.github.seqware.queryengine.model.interfaces
ACL.Builder() - Constructor for class com.github.seqware.queryengine.model.interfaces.ACL.Builder
ACL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
ACLable - Interface in com.github.seqware.queryengine.model.interfaces: Interface for object under access control.
action - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
actions - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Adag - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object: Adag object match to the element, which is a root element in a dax.
Adag(AbstractWorkflowDataModel) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
adapterCont - Class in net.sourceforge.seqware.pipeline.modules.qc: Basic QC report This module parses quality report from Illumina pipeline (Gerald) PE Adapters1 5' P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT PE PCR Primer 1.01 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3 PE PCR Primer 2.01 5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT PE Read 1 Sequencing Primer 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT PE Read 2 Sequencing Primer 5' CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT (1) Normally, PE read 2 is used for SE sequencing and 1st of PE in PE run and (2)PE read 1 will is used for 2nd of PE in PE run Underlying script: sw_module_adapterCont.pl (by Sara Grimm) Newly updated script: calculate_adapter_contamination.pl (by Sara Grimm) 6/2/2010 Necessary programs: perl Expected output: adapter_cont.txt
adapterCont() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.adapterCont
adapterspec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
adaptor - Variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser
add(Feature) - Method in class com.github.seqware.queryengine.model.FeatureSet: Add one element to the set
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.FeatureSet: Add numerous elements from within a set
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.FeatureList: add.
add(T) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet: Add one element to the set
add(Collection<T>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet: Add numerous elements from within a set
add(T...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet: Add an array of elements
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Add one element to the set
add(Feature...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Add an array of elements
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Add numerous elements from within a set
add(Tag) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: Add one element to the set
add(Collection<Tag>) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: Add numerous elements from within a set
add(Tag...) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: Add an array of elements
add(Feature) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Add one element to the set
add(Feature...) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Add an array of elements
add(Collection<Feature>) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Add numerous elements from within a set
add(T) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface: Add one element to the set
add(Collection<T>) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface: Add numerous elements from within a set
add(T...) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface: Add an array of elements
add(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService: add.
add(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl: add.
add(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO: add.
add(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate: add.
add(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate: add.
add(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate: add.
add(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO: add.
add(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO: add.
add(Experiment) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList: add.
add(File) - Method in class net.sourceforge.seqware.common.model.lists.FileList: add.
add(IUS) - Method in class net.sourceforge.seqware.common.model.lists.IUSList: add.
add(Lane) - Method in class net.sourceforge.seqware.common.model.lists.LaneList: add.
add(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList: add.
add(LibrarySource) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList: add.
add(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList: add.
add(Organism) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList: add.
add(Platform) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList: add.
add(Processing) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList: add.
add(ReturnValue) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList: add.
add(Sample) - Method in class net.sourceforge.seqware.common.model.lists.SampleList: add.
add(SequencerRun) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList: add.
add(Study) - Method in class net.sourceforge.seqware.common.model.lists.StudyList: add.
add(StudyType) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList: add.
add(Workflow) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList: add.
add(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList: add.
add(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList: add.
add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList: add.
add(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2: add.
add(String, String) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams: add.
add - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: add_empty_processing_event.
add_empty_processing_event(int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: add_empty_processing_event.
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: add_empty_processing_event.
add_empty_processing_event(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: add_empty_processing_event.
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: add_empty_processing_event_by_parent_accession.
add_empty_processing_event_by_parent_accession(int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: add_empty_processing_event_by_parent_accession.
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: add_empty_processing_event_by_parent_accession.
add_empty_processing_event_by_parent_accession(int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: add_empty_processing_event_by_parent_accession.
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: add_task_group.
add_task_group(int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: add_task_group.
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: add_task_group.
add_task_group(int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: add_task_group.
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: add_workflow_run.
add_workflow_run(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: add_workflow_run.
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: add_workflow_run.
add_workflow_run(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: add_workflow_run.
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: add_workflow_run_ancestor.
add_workflow_run_ancestor(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: add_workflow_run_ancestor.
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: add_workflow_run_ancestor.
add_workflow_run_ancestor(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: add_workflow_run_ancestor.
addACL(ACL) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addACL.
addAllAnalysisIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
addAllFeatures(Iterable<? extends QueryEngine.FeaturePB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
addAllFeatures(Iterable<? extends QESupporting.FSGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
addAllFeatureSetIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
addAllGrps(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
addAllReferenceIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
addAllRights(Iterable<? extends Boolean>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
addAllTags(Iterable<? extends QESupporting.TagPB>) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
addAllTags(Iterable<? extends QESupporting.TagPB>) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
addAllTagSpecIDs(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
addAllUsers(Iterable<? extends QESupporting.SGIDPB>) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
addAnalysisIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
addAnalysisIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
addAnalysisIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
addAnalysisIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
addAnalysisIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
addAnalysisIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
addAnalysisPlugin(AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addAnalysisPlugin.
addAnalysisSet(AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addAnalysisSet.
addArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
addArgument(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule: addArgument.
addArgumentPair(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule: addArgumentPair.
addAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource: addAttribute.
addAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource: addAttribute.
addDirectory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: create a user defined directory before all jobs started
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: addExperiment.
addExperiment(Integer, Integer, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: addExperiment.
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: addExperiment.
addExperiment(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: addExperiment.
addFeatures(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
addFeatures(int, QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
addFeatures(QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
addFeatures(int, QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
addFeatures(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
addFeatures(int, QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
addFeatures(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
addFeatures(int, QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
addFeaturesBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
addFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
addFeaturesBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
addFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
addFeatureSet(FeatureSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addFeatureSet.
addFeatureSetIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
addFeatureSetIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
addFeatureSetIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
addFeatureSetIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
addFeatureSetIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
addFeatureSetIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
addFile(SqwFile) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: add a job specific file for provision
addFile(SqwFile) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: add a job specific file
addGroup(Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addGroup.
addGrps(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
addGrps(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
addGrps(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
addGrps(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
addGrpsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
addGrpsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
addIUS(Integer, Integer, String, String, String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: addSample.
addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
addIUS(Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
addJobs(AbstractJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow: add job to the workflow
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: addSample.
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
addLane(Integer, Integer, Integer, Integer, Integer, String, String, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
addParent(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
addParent(AbstractJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: add a parent
addParent(Job) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
addParent(Job) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: add job's parent
addParentAccessionFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
addProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.Lane: addProcessing.
addProcessings(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems: addProcessings.
addReference(Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addReference.
addReferenceIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
addReferenceIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
addReferenceIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
addReferenceIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
addReferenceIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
addReferenceIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
addReferenceSet(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addReferenceSet.
addRequirement(Requirement) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
AddRGTags - Class in net.sourceforge.seqware.pipeline.modules.BamFilters: Annotate BAM file with read group tags.
AddRGTags() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags
addRights(boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
addRow(Flexigrid.Cells) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: addRow.
addSample(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: addSample.
addSample(Integer, Integer, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: addSample.
addSample(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: addSample.
addSample(Integer, Integer, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: addSample.
addSequencerRun(Integer, String, String, boolean, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
addSequencerRun(Integer, String, String, boolean, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: addSample.
addSequencerRun(Integer, String, String, boolean, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
addSequencerRun(Integer, String, String, boolean, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: FIXME: there are problems with setting accession when I should set ID
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: addStudy.
addStudy(String, String, String, StudyType, String, String, Integer) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: addStudy.
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: addStudy.
addStudy(String, String, String, StudyType, String, String, Integer) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: addStudy.
addTag(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: addTag.
addTag(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: addTag.
addTags(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
addTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
addTags(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
addTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
addTags(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
addTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
addTags(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
addTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
addTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: addTags.
addTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: addTags.
addTagsBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
addTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
addTagsBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
addTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
addTagSet(TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addTagSet.
addTagSpecIDs(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
addTagSpecIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
addTagSpecIDs(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
addTagSpecIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
addTagSpecIDsBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
addTagSpecIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
addTest(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow: add a test command for the workflow
addUser(User) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addUser.
addUsers(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
addUsers(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
addUsers(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
addUsers(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
addUsersBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
addUsersBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
addUserToGroup(User, Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: addUserToGroup.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: addWorkflow.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: addWorkflow.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: addWorkflow.
addWorkflow(String, String, String, String, String, String, String, boolean, String, boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: addWorkflow.
addWorkflowRun(String, String, String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
addWorkflowRunParam(int, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: addWorkflowRunParam.
ADHOC_TAGSETS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant ADHOC_TAGSETS_PARAM='a'
adhoctagset - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
algorithm - Variable in class net.sourceforge.seqware.common.module.ReturnValue
algorithmName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
alias - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
AlignmentQualityReportDecider - Class in net.sourceforge.seqware.pipeline.deciders: FIXME: this extends the plugin but really it should be a decider subclass.
AlignmentQualityReportDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider
alignStat - Class in net.sourceforge.seqware.pipeline.modules.qc: Performing post alignment per lane based counting Underlying script: sw_module_alignStat.pl Necessary programs: perl, java, Picard (SamFormatConverter.jar) Output: ~.mapped.txt tab-delimited files in four columns: bam file name, raw read count, mapped read count and aligned percentage (%)
alignStat() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.alignStat
AnalisysBulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller: AnalisysBulkDownloadListController class.
AnalisysBulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController: Constructor for AnalisysBulkDownloadListController.
AnalisysBulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller: AnalisysBulkDownloadListDetailsController class.
AnalisysBulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Constructor for AnalisysBulkDownloadListDetailsController.
AnalisysEventController - Class in net.sourceforge.solexatools.webapp.controller: StudyController
AnalisysEventController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Constructor for AnalisysEventController.
AnalisysEventController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Constructor for AnalisysEventController.
AnalisysListController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
AnalisysListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListController: Constructor for AnalisysListController.
AnalisysListDetailsController - Class in net.sourceforge.solexatools.webapp.controller: AnalisysListDetailsController class.
AnalisysListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Constructor for AnalisysListDetailsController.
AnalisysRunningListDetailsController - Class in net.sourceforge.solexatools.webapp.controller: AnalisysRunningListDetailsController class.
AnalisysRunningListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Constructor for AnalisysRunningListDetailsController.
AnalisysTableController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
AnalisysTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysTableController: Constructor for AnalisysListController.
AnalisysTableControllerDetails - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
AnalisysTableControllerDetails() - Constructor for class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails: Constructor for AnalisysListController.
Analysis<ReturnType> - Class in com.github.seqware.queryengine.model: An Analysis object represents specific calls to analysis components, most of which will be implemented as an analysis plug-in on the backend.
Analysis() - Constructor for class com.github.seqware.queryengine.model.Analysis: Create a new analysis
analysis - Variable in class com.github.seqware.queryengine.model.Analysis.Builder
analysis - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
Analysis.Builder - Class in com.github.seqware.queryengine.model
Analysis.Builder() - Constructor for class com.github.seqware.queryengine.model.Analysis.Builder
ANALYSIS_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant: Constant ANALYSIS_VIEW="redirect:/myAnalisysList.htm"
analysisattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
analysisattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
analysisCenter - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
analysisfiles - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
ANALYSISIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
AnalysisIO - Class in com.github.seqware.queryengine.impl.protobufIO: Place-holder
AnalysisIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO
analysislink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
analysislinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
AnalysisPluginInterface<T> - Interface in com.github.seqware.queryengine.plugins: This will describe the interface custom plugins must conform to.
AnalysisPluginInterface.ReturnValue - Class in com.github.seqware.queryengine.plugins
AnalysisPluginInterface.ReturnValue() - Constructor for class com.github.seqware.queryengine.plugins.AnalysisPluginInterface.ReturnValue
AnalysisSet - Interface in com.github.seqware.queryengine.model: An AnalysisSet object groups analysis events that are created by software suites or related tools.
AnalysisSet - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet
AnalysisSet.Builder - Class in com.github.seqware.queryengine.model
AnalysisSet.Builder() - Constructor for class com.github.seqware.queryengine.model.AnalysisSet.Builder
AnalysisSetIO - Class in com.github.seqware.queryengine.impl.protobufIO: AnalysisSetIO class.
AnalysisSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO
AnalysisType - Class in net.sourceforge.seqware.queryengine.webservice.model: A SRA analysis object captures secondary analysis results from a short read dataset.
AnalysisType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
analysistype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
AnalysisType.ANALYSISATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
AnalysisType.ANALYSISFILES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISFILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
AnalysisType.ANALYSISFILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISFILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
AnalysisType.ANALYSISLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS
AnalysisType.ANALYSISLINKS.ANALYSISLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
AnalysisType.ANALYSISTYPE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.ANALYSISTYPE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
AnalysisType.PARENT - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.PARENT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
AnalysisType.PARENT.EXPERIMENTREF - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.PARENT.EXPERIMENTREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
AnalysisType.PARENT.RUNREF - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.PARENT.RUNREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
AnalysisType.PARENT.SAMPLEPOOLREF - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEPOOLREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
AnalysisType.PARENT.SAMPLEREF - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.PARENT.SAMPLEREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
AnalysisType.PARENT.STUDYREF - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
AnalysisType.PARENT.STUDYREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
AND - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant AND=4
AND - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant AND=4
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateExperiment.
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateExperiment.
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateExperiment.
annotateExperiment(int, ExperimentAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateExperiment.
annotateExperiment(int, Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateExperiment.
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateIUS.
annotateIUS(int, IUSAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateIUS.
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateIUS.
annotateIUS(int, IUSAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateIUS.
annotateIUS(int, Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateIUS.
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateLane.
annotateLane(int, LaneAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateLane.
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateLane.
annotateLane(int, LaneAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateLane.
annotateLane(int, Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateLane.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateProcessing.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateProcessing.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateProcessing.
annotateProcessing(int, ProcessingAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateProcessing.
annotateProcessing(int, Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateProcessing.
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateSample.
annotateSample(int, SampleAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateSample.
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateSample.
annotateSample(int, SampleAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateSample.
annotateSample(int, Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateSample.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateSequencerRun.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateSequencerRun.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateSequencerRun.
annotateSequencerRun(int, SequencerRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateSequencerRun.
annotateSequencerRun(int, Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateSequencerRun.
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateStudy.
annotateStudy(int, StudyAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateStudy.
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateStudy.
annotateStudy(int, StudyAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateStudy.
annotateStudy(int, Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateStudy.
AnnotateVariantDB - Class in net.sourceforge.seqware.pipeline.modules.queryengine: Purpose: This module uses the VariantConsequenceImporter and TagAnnotationImporter from the SeqWare QueryEngine Backend project to annotate with coding consequence and dbSNP status.
AnnotateVariantDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB
AnnotateVariantsWithContigAndZygosity - Class in net.sourceforge.seqware.queryengine.tools.annotators: AnnotateVariantsWithContigAndZygosity class.
AnnotateVariantsWithContigAndZygosity() - Constructor for class net.sourceforge.seqware.queryengine.tools.annotators.AnnotateVariantsWithContigAndZygosity
AnnotateWithCodingConsequence - Class in net.sourceforge.seqware.pipeline.modules.queryengine: Purpose: This module uses perl annotation scripts from SeqWare Pipeline to annotate with coding consequence status and then generates annotations tag files for loading in the database.
AnnotateWithCodingConsequence() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence
AnnotateWithDbSNP - Class in net.sourceforge.seqware.pipeline.modules.queryengine: Purpose: This module uses an existing variant database, dumps the variants as a BED file, uses perl annotation scripts from SeqWare Pipeline to annotate with dbSNP status, and create a load file that can be loaded back into the DB.
AnnotateWithDbSNP() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateWorkflow.
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateWorkflow.
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateWorkflow.
annotateWorkflow(int, WorkflowAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateWorkflow.
annotateWorkflow(int, Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateWorkflow.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: annotateWorkflowRun.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: annotateWorkflowRun.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: annotateWorkflowRun.
annotateWorkflowRun(int, WorkflowRunAttribute, Boolean) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateWorkflowRun.
annotateWorkflowRun(int, Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: annotateWorkflowRun.
annotationAwareAspectJAutoProxyCreator() - Method in class net.sourceforge.seqware.pipeline.runner.Runner2.ModuleConfig
anonymizedname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
ApacheSerialization - Class in com.github.seqware.queryengine.impl: ApacheSerialization class.
ApacheSerialization() - Constructor for class com.github.seqware.queryengine.impl.ApacheSerialization
APP - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
appID - Variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
Argument - Class in net.sourceforge.seqware.pipeline.workflowV2.model: Argument class.
Argument(String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Argument: Constructor for Argument.
asDto(SampleSearch) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: asDto.
asDto(Attribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: asDto.
asDto(Registration) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: asDto.
asDto(Sample) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: asDto.
asDto(IUS) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: asDto.
asDto(File) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: asDto.
aSet - Variable in class com.github.seqware.queryengine.model.AnalysisSet.Builder
aSet - Variable in class com.github.seqware.queryengine.model.FeatureSet.Builder
aSet - Variable in class com.github.seqware.queryengine.model.Group.Builder
aSet - Variable in class com.github.seqware.queryengine.model.ReferenceSet.Builder
aSet - Variable in class com.github.seqware.queryengine.model.TagSet.Builder
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: associate_processing_event_with_parents_and_child.
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: associate_processing_event_with_parents_and_child.
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: associate_processing_event_with_parents_and_child.
associate_processing_event_with_parents_and_child(int, int[], int[]) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: associate_processing_event_with_parents_and_child.
associateTag(Tag) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: associate new tag to a subject with a null value and a null predicate
associateTag(Tag) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable: associate new tag to a subject with a null value and a null predicate
associateTag(Tag) - Method in class com.github.seqware.queryengine.model.Tag: associate new tag to a subject with a null value and a null predicate
atDto(Organism) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: atDto.
Atom<T extends Atom> - Interface in com.github.seqware.queryengine.model: Implements core functionality that is shared by all classes that require tags.
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
ATOM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
AtomImpl<T extends Atom> - Class in com.github.seqware.queryengine.model.impl: Implements core functionality that is shared by all classes that require tags.
AtomImpl() - Constructor for class com.github.seqware.queryengine.model.impl.AtomImpl: Constructor for AtomImpl.
AtomImpl.TagValueIterable - Class in com.github.seqware.queryengine.model.impl
AtomImpl.TagValueIterable(Map<String, Map<String, Tag>>) - Constructor for class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterable
AtomImpl.TagValueIterator - Class in com.github.seqware.queryengine.model.impl
AtomImpl.TagValueIterator(Map<String, Map<String, Tag>>) - Constructor for class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
atomStateChange(Atom, CreateUpdateManager.State) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Called by Atoms when they need to change state (for example, to notify that they have become a dirty new version)
atomStateChange(Atom, CreateUpdateManager.State) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Called by Atoms when they need to change state (for example, to notify that they have become a dirty new version)
Attribute - Interface in net.sourceforge.seqware.common.model: Attribute interface.
attribute - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
AttributeAnnotator - Class in net.sourceforge.seqware.pipeline.plugins: AttributeAnnotator class.
AttributeAnnotator() - Constructor for class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator: Constructor for AttributeAnnotator.
AttributeDto - Class in net.sourceforge.seqware.webservice.dto
AttributeDto() - Constructor for class net.sourceforge.seqware.webservice.dto.AttributeDto
attributes - Variable in class net.sourceforge.seqware.common.module.ReturnValue
authenticate() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource: authenticate.
authenticate(String) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet: authenticate.
Authentication - Class in net.sourceforge.solexatools.authentication: Abstract Authentication class.
Authentication() - Constructor for class net.sourceforge.solexatools.authentication.Authentication
AUTOFLUSH - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: Constant AUTOFLUSH=false
available - Variable in class com.github.seqware.queryengine.system.importers.Importer
available - Variable in class net.sourceforge.seqware.queryengine.tools.importers.Importer

B

BackEndInterface - Interface in com.github.seqware.queryengine.impl: This interface specifies operations to persist, update, and add objects to the back-end without knowing about the specific database back-end.
BackendPool - Class in net.sourceforge.seqware.queryengine.webservice.model: BackendPool class.
BackendPool() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.BackendPool
BadFile - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode: Constant BadFile=3
BadModule - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode: Constant BadModule=4
BadParameter - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode: Constant BadParameter=2
BadRunnerParams - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode: Constant BadRunnerParams=5
BAM2Count - Class in net.sourceforge.seqware.pipeline.modules.quantification: Get gene level count from BAM file.
BAM2Count() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count
barcodeSeqence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
BaseBuilder<S,T extends BaseBuilder> - Class in com.github.seqware.queryengine.model.interfaces: Builders are used to construct Atom.
BaseBuilder() - Constructor for class com.github.seqware.queryengine.model.interfaces.BaseBuilder
basecaller - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
basecalls - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
basecoord - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
basedir - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
baseQualities - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
BashJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
BashJob(String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.BashJob
BasicDecider - Class in net.sourceforge.seqware.pipeline.deciders
BasicDecider() - Constructor for class net.sourceforge.seqware.pipeline.deciders.BasicDecider
basicQC - Class in net.sourceforge.seqware.pipeline.modules.qc: Purpose: This module generates pre and post alignment QC reports using dqc from the DNAA package.
basicQC() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.basicQC
BasicResource - Class in net.sourceforge.seqware.webservice.resources: See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource
BasicResource() - Constructor for class net.sourceforge.seqware.webservice.resources.BasicResource: Constructor for BasicResource.
BasicRestlet - Class in net.sourceforge.seqware.webservice.resources: See https://sourceforge.net/apps/mediawiki/seqware/index.php?title=How_to_extend_the_web_service#Basic_Resource
BasicRestlet(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.BasicRestlet: Constructor for BasicRestlet.
BasicWorkflow - Class in net.sourceforge.seqware.pipeline.workflow: Abstract BasicWorkflow class.
BasicWorkflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow: Constructor for BasicWorkflow.
BasicWorkflow.Job - Enum in net.sourceforge.seqware.pipeline.workflow
BATCH_SIZE - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant BATCH_SIZE=100000
batch_size - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
BATCH_SIZE_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant BATCH_SIZE_PARAM='b'
BCtrend - Class in net.sourceforge.seqware.pipeline.modules.qc: Performing per lane based statistics Underlying script: sw_module_BCtrend.pl Necessary programs: perl Expected output: read_depth.txt
BCtrend() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.BCtrend
BeanFactory - Class in net.sourceforge.seqware.common.factory: Abstract BeanFactory class.
BeanFactory() - Constructor for class net.sourceforge.seqware.common.factory.BeanFactory
BEDExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters: BEDExporter class.
BEDExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.BEDExporter
BedFeatureImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: BedFeatureImportWorker class.
BedFeatureImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.BedFeatureImportWorker: Constructor for BedFeatureImportWorker.
benchmark() - Method in class com.github.seqware.queryengine.tutorial.Poster: benchmark.
benchmark() - Method in class com.github.seqware.queryengine.tutorial.PosterSGE: benchmark.
BENCHMARKING_BATCH_SIZE - Static variable in class com.github.seqware.queryengine.tutorial.Poster: Constant BENCHMARKING_BATCH_SIZE=20000
BENCHMARKING_BATCH_SIZE - Static variable in class com.github.seqware.queryengine.tutorial.PosterSGE: Constant BENCHMARKING_BATCH_SIZE=20000
BerkeleyDBFactory - Class in net.sourceforge.seqware.queryengine.backend.factory.impl: BerkeleyDBFactory class.
BerkeleyDBFactory() - Constructor for class net.sourceforge.seqware.queryengine.backend.factory.impl.BerkeleyDBFactory
BerkeleyDBStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl: BerkeleyDBStore class.
BerkeleyDBStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore
Bfast - Class in net.sourceforge.seqware.pipeline.modules.alignment: Bfast class.
Bfast() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.Bfast
biMap - Variable in class com.github.seqware.queryengine.impl.ProtobufSerialization
bind(HttpServletRequest, Object) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
bindSessionToThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions: bindSessionToThread.
bindSessionToThread(FlushMode) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions: bindSessionToThread.
binSize - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
BlobReaderWriter - Class in net.sourceforge.seqware.queryengine.prototypes: BlobReaderWriter class.
BlobReaderWriter() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.BlobReaderWriter
blockCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
blockSizes - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
blockStarts - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
bmfsplit - Class in net.sourceforge.seqware.pipeline.modules: bmfsplit class.
bmfsplit() - Constructor for class net.sourceforge.seqware.pipeline.modules.bmfsplit
BRACKET_CLOSE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant BRACKET_CLOSE=5
BRACKET_CLOSE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant BRACKET_CLOSE=5
BRACKET_OPEN - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant BRACKET_OPEN=6
BRACKET_OPEN - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant BRACKET_OPEN=6
BrianTest - Class in com.github.seqware.queryengine.tutorial: This is a quick and sample application built on top of our API, created during the August 9th Hackathon.
BrianTest(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.BrianTest: Constructor for BrianTest.
brokerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
BufferedReaderThread - Class in net.sourceforge.seqware.common.util.iotools: BufferedReaderThread class.
BufferedReaderThread(InputStream) - Constructor for class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread: Constructor for BufferedReaderThread.
BUFFERSIZE - Static variable in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController: Constant BUFFERSIZE=500*1024
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
build() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
build() - Method in class com.github.seqware.queryengine.model.Analysis.Builder
build() - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
build() - Method in class com.github.seqware.queryengine.model.Feature.Builder
build() - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
build() - Method in class com.github.seqware.queryengine.model.Group.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.Group.Builder
build() - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl.Builder
build() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
build() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
build() - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
build() - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder: Build a Atom
build() - Method in class com.github.seqware.queryengine.model.Reference.Builder
build() - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
build() - Method in class com.github.seqware.queryengine.model.Tag.Builder
build() - Method in class com.github.seqware.queryengine.model.TagSet.Builder
build(boolean) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
build() - Method in class com.github.seqware.queryengine.model.User.Builder
Buildable<T extends BaseBuilder> - Interface in com.github.seqware.queryengine.model.interfaces: An interface for the various builders that we will use to construct models for managed objects
buildAnalysis() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a new analysis
buildAnalysis() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a new analysis
buildAnalysisSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build an analysis set
buildAnalysisSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build an analysis set
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaJob
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob: for overridden by a specific job type
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusPerlJob
buildCommandString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
buildDirectory(File) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil: buildDirectory.
buildFeature() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a feature
buildFeature() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a feature
buildFeatureSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a featureSet with a reference
buildFeatureSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a featureSet with a reference
buildFeatureSetInternal() - Method in class com.github.seqware.queryengine.impl.MRHBaseModelManager: buildFeatureSetInternal.
buildFeatureSetInternal() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: buildFeatureSetInternal.
buildGroup() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a group
buildGroup() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a group
buildMetadataString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
buildPartial() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
buildReference() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a Reference with a given name
buildReference() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a Reference with a given name
buildReferenceSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a new reference set
buildReferenceSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a new reference set
buildTag() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a Tag
buildTag() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a Tag
buildTagSet() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a set of tags
buildTagSet() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a set of tags
buildUser() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Build a user
buildUser() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Build a user
buildWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: to be Overridden by the workflow author
buildWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.XmlWorkflowDataModel
BulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller: BulkDownloaderController class.
BulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController: Constructor for BulkDownloaderController.
BulkDownloaderSizeValidatorController - Class in net.sourceforge.solexatools.webapp.controller: BulkDownloaderSizeValidatorController class.
BulkDownloaderSizeValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController
BulkDownloadListController - Class in net.sourceforge.solexatools.webapp.controller: BulkDownloadListController class.
BulkDownloadListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController: Constructor for BulkDownloadListController.
BulkDownloadListDetailsController - Class in net.sourceforge.solexatools.webapp.controller: BulkDownloadListDetailsController class.
BulkDownloadListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Constructor for BulkDownloadListDetailsController.
BulkProvisionFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities: Purpose: This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket URL, HTTP/HTTPS URL, or local directory path).
BulkProvisionFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles
BulkUtil - Class in net.sourceforge.solexatools.util: BulkUtil class.
BulkUtil() - Constructor for class net.sourceforge.solexatools.util.BulkUtil
Bundle - Class in net.sourceforge.seqware.pipeline.bundle: This is a utility class that lets you manipulate a workflow bundle.
Bundle() - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle: Constructor for Bundle.
Bundle(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.bundle.Bundle: Constructor for Bundle.
bundleDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
BundleInfo - Class in net.sourceforge.seqware.pipeline.bundle: BundleInfo class.
BundleInfo() - Constructor for class net.sourceforge.seqware.pipeline.bundle.BundleInfo
BundleManager - Class in net.sourceforge.seqware.pipeline.plugins: BundleManager class.
BundleManager() - Constructor for class net.sourceforge.seqware.pipeline.plugins.BundleManager: Constructor for BundleManager.
bundleUtil - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
BWA - Class in net.sourceforge.seqware.pipeline.modules.alignment: Align reads via BWA.
BWA() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.BWA
BWA_0_5_9 - Class in net.sourceforge.seqware.pipeline.modules.alignment.bwa: Align reads via BWA.
BWA_0_5_9() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9
byte2HexString(byte[]) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: byte2HexString.
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: Constant BYTEA=1
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: Constant BYTEA=1
BYTEA - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Constant BYTEA=1
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO: Convert from protein buffer object in byte array to model.
byteArr2m(byte[]) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO: Convert from protein buffer object in byte array to model.

C

CachedTagResource - Class in net.sourceforge.seqware.queryengine.webservice.view: CachedTagResource class.
CachedTagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CachedTagResource
calculateTotalTime(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport: calculateTotalTime.
calledBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
calledBaseCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
calledBaseCountForward - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
calledBaseCountReverse - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
callOne - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
callTwo - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
CancelAnalysisWorkflowController - Class in net.sourceforge.solexatools.webapp.controller: CancelAnalysisWorkflowController class.
CancelAnalysisWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController: Constructor for CancelAnalysisWorkflowController.
CancelBulkDownloaderController - Class in net.sourceforge.solexatools.webapp.controller: CancelBulkDownloaderController class.
CancelBulkDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController: Constructor for CancelBulkDownloaderController.
CancelInputDownloaderController - Class in net.sourceforge.solexatools.webapp.controller: CancelInputDownloaderController class.
CancelInputDownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController: Constructor for CancelInputDownloaderController.
CASCADE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
causedBy(Throwable, Class) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools: causedBy.
centerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
centername - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
centerName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
centerprojectname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
cfg - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
ChangeNumberPopupPageController - Class in net.sourceforge.solexatools.webapp.controller: ChangeNumberPopupPageController class.
ChangeNumberPopupPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController: Constructor for ChangeNumberPopupPageController.
ChangeWorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller: ChangeWorkflowParamValueController class.
ChangeWorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController: Constructor for ChangeWorkflowParamValueController.
CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant CHECK="check"
CHECK - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Constant CHECK="check"
checkExit(int) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
checkFileDetails(ReturnValue, FileMetadata) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider: Performs any additional checks on the file before adding it to the list of files to incorporate.
CheckForCycles - Class in net.sourceforge.seqware.common.hibernate: CheckForCycles class.
CheckForCycles() - Constructor for class net.sourceforge.seqware.common.hibernate.CheckForCycles
checkFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder: Check a row key
checkOutput(String) - Static method in class com.github.seqware.queryengine.system.Utility: Check whether we can create the output for a particular filename
checkPassword(String) - Method in class com.github.seqware.queryengine.model.User: Check a user's password
checkPermission(Permission) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
checkPermission(Permission, Object) - Method in class net.sourceforge.seqware.common.util.NoExitSecurityManager
checkpoint() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: checkpoint.
checkProcessing(Processing) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles: checkProcessing.
checkSample(Sample) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles: checkSample.
checkStudy(Integer) - Method in class net.sourceforge.seqware.common.hibernate.CheckForCycles: checkStudy.
checksum - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
checksumMethod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
childMaps - Variable in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
childTags - Variable in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: clean_up.
clean_up() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: clean_up.
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: clean_up.
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: clean_up.
clean_up() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
clean_up() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
clean_up() - Method in class net.sourceforge.seqware.pipeline.module.Module: clean_up.
clean_up() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: clean_up.
clean_up() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: clean_up.
clean_up() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter: Perform post-task clean-up here.
clean_up() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker: Perform post-task clean-up here.
cleanup() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: cleanup.
cleanup() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: cleanup.
cleanup() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: cleanup.
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
clear() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clear() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Erase the current set of managed models without saving them to the back-end
clear() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Erase the current set of managed models without saving them to the back-end
clearAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
clearAnalysisIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
clearAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
clearDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
clearDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clearDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clearEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
clearFeatures() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
clearFeatures() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clearFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
clearFeatureSetIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
clearFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
clearGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
clearGrps() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
clearMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clearName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
clearOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clearParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
clearPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
clearPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
clearPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clearPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clearReferenceIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clearRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
clearRights() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
clearRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
clearScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
clearSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
clearSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
clearSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearStorage() - Method in class com.github.seqware.queryengine.impl.HBaseStorage: For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStorage() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStorage() - Method in class com.github.seqware.queryengine.impl.StorageInterface: For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStorage() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: For debugging or testing purposes, this will wipe out all objects in the serialization store
clearStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearTags() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
clearTags() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
clearTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearTagSpecIDs() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
clearTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
clearTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
clearType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clearUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
clearUsers() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clearVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clearVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
cli2Map(String[], Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: Method to getValues all "--key=value" or "--key value" parameters and add them to hashmap
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
clone() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
clone(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing: clone.
clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
clone() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.File: cloneFromDB.
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.Processing: cloneFromDB.
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.Registration: cloneFromDB.
cloneFromDB(int) - Static method in class net.sourceforge.seqware.common.model.WorkflowRun: cloneFromDB.
cloneToHibernate(Processing) - Static method in class net.sourceforge.seqware.common.model.Processing: cloneToHibernate.
cloneToHibernate(WorkflowRun) - Static method in class net.sourceforge.seqware.common.model.WorkflowRun: cloneToHibernate.
close() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Convenience method to flush() all entities and clear().
close() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Convenience method to flush() all entities and clear().
close() - Static method in class net.sourceforge.seqware.common.factory.DBAccess: close.
close() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: close.
close() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: close.
close() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: close.
close() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator: close.
closeImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator: Closes the database iterator.
closeImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator: Closes the database iterator.
closeStorage() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory: Close the currently operating storage method
closeStorage() - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Some storage types should be explicitly told when shutting down to release resources.
closeStorage() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Some storage types should be explicitly told when shutting down to release resources.
closeStorage() - Method in class com.github.seqware.queryengine.impl.StorageInterface: Some storage types should be explicitly told when shutting down to release resources.
closeStorage() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Some storage types should be explicitly told when shutting down to release resources.
codingStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
codingStop - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
collectFlags - Class in net.sourceforge.seqware.pipeline.modules.qc: Collecting flag information per lane Underlying script: sw_module_extractFlag.pl Necessary programs: perl Expected output: flowcell.lane.flagCollection.txt
collectFlags() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.collectFlags
collectProcessingList(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource: collectProcessingList.
color - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
colormatrix - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
colormatrixcode - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
com.github.seqware.queryengine - package com.github.seqware.queryengine: The base directory for the SeqWare Query Engine, we only have constants defined here for now.
com.github.seqware.queryengine.dto - package com.github.seqware.queryengine.dto
com.github.seqware.queryengine.factory - package com.github.seqware.queryengine.factory: Provides the classes that the RESTful interface will use to construct interfaces that use the back-end without reference to the specific back-end.
com.github.seqware.queryengine.impl - package com.github.seqware.queryengine.impl: Provides the classes that implement the actual back-end for various database (or lack of database) types
com.github.seqware.queryengine.impl.protobufIO - package com.github.seqware.queryengine.impl.protobufIO: This package contains the classes that specifically handle protobuffer serialization to and from the back-end.
com.github.seqware.queryengine.impl.tuplebinderIO - package com.github.seqware.queryengine.impl.tuplebinderIO: This package contains the a couple of experimental classes that would have to be substantially added to in order to add BerkeleyDB serialization support.
com.github.seqware.queryengine.kernel - package com.github.seqware.queryengine.kernel: This package contains supporting classes for Queries.
com.github.seqware.queryengine.kernel.output - package com.github.seqware.queryengine.kernel.output
com.github.seqware.queryengine.model - package com.github.seqware.queryengine.model: Provides the classes that the RESTful API will interact with.
com.github.seqware.queryengine.model.impl - package com.github.seqware.queryengine.model.impl: Provides the classes that implement model entities that the RESTful interface will interact with
com.github.seqware.queryengine.model.impl.hbasemrlazy - package com.github.seqware.queryengine.model.impl.hbasemrlazy: Provides classes that 'lazily' allow their members to persist their own membership and use Map/Reduce to determine attributes about themselves.
com.github.seqware.queryengine.model.impl.inMemory - package com.github.seqware.queryengine.model.impl.inMemory: Provides classes that support a simple in-memory implementation of the various model classes.
com.github.seqware.queryengine.model.impl.lazy - package com.github.seqware.queryengine.model.impl.lazy: Provides classes that 'lazily' allow their members to persist their own membership.
com.github.seqware.queryengine.model.interfaces - package com.github.seqware.queryengine.model.interfaces
com.github.seqware.queryengine.plugins - package com.github.seqware.queryengine.plugins: Provides the interfaces that an external plugin developer would need to conform to in order for the Query Engine to install and run properly.
com.github.seqware.queryengine.plugins.hbasemr - package com.github.seqware.queryengine.plugins.hbasemr: Provides classes that support and implement hbase implementations of plug-ins.
com.github.seqware.queryengine.plugins.inmemory - package com.github.seqware.queryengine.plugins.inmemory: Provides classes that support and implement in-memory mock-ups for plugins.
com.github.seqware.queryengine.plugins.lazyinmemory - package com.github.seqware.queryengine.plugins.lazyinmemory: Provides classes that support and implement in-memory mock-ups for plugins while being aware of lazy classes.
com.github.seqware.queryengine.system - package com.github.seqware.queryengine.system
com.github.seqware.queryengine.system.exporters - package com.github.seqware.queryengine.system.exporters: Command-line tools for exporting files to external file types.
com.github.seqware.queryengine.system.importers - package com.github.seqware.queryengine.system.importers: Command-line tools for importing files from external file types.
com.github.seqware.queryengine.system.importers.workers - package com.github.seqware.queryengine.system.importers.workers: Multi-threaded workers that handle the actual work for the FeatureImporter when exporting to various external file types.
com.github.seqware.queryengine.tutorial - package com.github.seqware.queryengine.tutorial: Classes for testing and hacking new tools.
com.github.seqware.queryengine.util - package com.github.seqware.queryengine.util: Provides utility classes for accessing this API via the model
com.github.seqware.queryengine.util.obo - package com.github.seqware.queryengine.util.obo
Command - Class in net.sourceforge.seqware.pipeline.workflowV2.model
Command() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Command
commaSeparateMy(Collection<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
comment() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: comment.
COMMENT_EOL - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant COMMENT_EOL=7
COMMENT_EOL - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant COMMENT_EOL=7
COMMENT_INLINE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant COMMENT_INLINE=8
COMMENT_INLINE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant COMMENT_INLINE=8
commonname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
commonTimestamp - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
compare(ExperimentSpotDesignReadSpec, ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.ContigPositionComparator
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.IntegerIdComparator
compare(Object, Object) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.TagComparator
CompareDatabasesWithROC - Class in net.sourceforge.seqware.queryengine.examples: CompareDatabasesWithROC class.
CompareDatabasesWithROC() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC
CompareDatabasesWithROCHBase - Class in net.sourceforge.seqware.queryengine.examples: CompareDatabasesWithROCHBase class.
CompareDatabasesWithROCHBase() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase
CompareDatabasesWithROCOld - Class in net.sourceforge.seqware.queryengine.examples: CompareDatabasesWithROCOld class.
CompareDatabasesWithROCOld() - Constructor for class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCOld
compareTo(SequencerRunReport.Row) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
compareTo(Expense) - Method in class net.sourceforge.seqware.common.model.Expense
compareTo(Experiment) - Method in class net.sourceforge.seqware.common.model.Experiment
compareTo(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
compareTo(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: compareTo.
compareTo(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: compareTo.
compareTo(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
compareTo(File) - Method in class net.sourceforge.seqware.common.model.File
compareTo(FileType) - Method in class net.sourceforge.seqware.common.model.FileType
compareTo(Invoice) - Method in class net.sourceforge.seqware.common.model.Invoice
compareTo(IUS) - Method in class net.sourceforge.seqware.common.model.IUS
compareTo(IUSAttribute) - Method in class net.sourceforge.seqware.common.model.IUSAttribute
compareTo(Lane) - Method in class net.sourceforge.seqware.common.model.Lane
compareTo(LaneAttribute) - Method in class net.sourceforge.seqware.common.model.LaneAttribute
compareTo(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
compareTo(LibrarySource) - Method in class net.sourceforge.seqware.common.model.LibrarySource
compareTo(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
compareTo(Organism) - Method in class net.sourceforge.seqware.common.model.Organism
compareTo(Platform) - Method in class net.sourceforge.seqware.common.model.Platform
compareTo(Processing) - Method in class net.sourceforge.seqware.common.model.Processing
compareTo(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
compareTo(Registration) - Method in class net.sourceforge.seqware.common.model.Registration
compareTo(Sample) - Method in class net.sourceforge.seqware.common.model.Sample
compareTo(SampleAttribute) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
compareTo(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRun
compareTo(SequencerRunAttribute) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
compareTo(ShareStudy) - Method in class net.sourceforge.seqware.common.model.ShareStudy
compareTo(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
compareTo(Study) - Method in class net.sourceforge.seqware.common.model.Study: compareTo.
compareTo(StudyAttribute) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
compareTo(StudyType) - Method in class net.sourceforge.seqware.common.model.StudyType: compareTo.
compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.Workflow
compareTo(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute
compareTo(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
compareTo(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
compareTo(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: compareTo.
compareTo(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
compareTo(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute
compareTo(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
compareTo(StudySampleReportFileLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem
compareTo(StudySampleReportLineItem) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem
CompareTwoVariantAndCoverageDatabases - Class in net.sourceforge.seqware.queryengine.tools.reporters: CompareTwoVariantAndCoverageDatabases class.
CompareTwoVariantAndCoverageDatabases() - Constructor for class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantAndCoverageDatabases
CompareTwoVariantDatabases - Class in net.sourceforge.seqware.queryengine.tools.reporters: CompareTwoVariantDatabases class.
CompareTwoVariantDatabases() - Constructor for class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantDatabases
compareWorkflowRunFiles(String, List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider: Tests if the files from the workflow run (workflowRunAcc) are the same as those found in the database (filesToRun).
comparison() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: comparison.
compileQuery(String) - Static method in class com.github.seqware.queryengine.kernel.RPNStack: Compiles the given query string that adheres to the syntax of SeqWareQueryLanguage.g and returns a RPNStack object representing the query.
COMPLETED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant COMPLETED="completed"
Compress - Class in net.sourceforge.seqware.pipeline.modules.utilities: Purpose: This module extends allows for compressing and decompressing files.
Compress() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.Compress
compressed - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
COMPRESSED_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant COMPRESSED_PARAM='c'
Compression - Class in com.github.seqware.queryengine.kernel: Static methods for compressing/decompressing user data.
Compression() - Constructor for class com.github.seqware.queryengine.kernel.Compression
config - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
config - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
config - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
config - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
config - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
configs - Variable in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
ConfigTools - Class in net.sourceforge.seqware.common.util.configtools: ConfigTools class.
ConfigTools() - Constructor for class net.sourceforge.seqware.common.util.configtools.ConfigTools
configureHBaseConfig(Configuration) - Static method in class com.github.seqware.queryengine.impl.HBaseStorage: Configure a HBaseConfiguration with a given set of properties
consensusAveSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
consensusBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
consensusCallQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
consensusMaxSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
Consequence - Class in net.sourceforge.seqware.queryengine.backend.model: Consequence class.
Consequence() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Consequence
CONSEQUENCE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model: Constant CONSEQUENCE=60
ConsequenceResource - Class in net.sourceforge.seqware.queryengine.webservice.view: ConsequenceResource class.
ConsequenceResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.ConsequenceResource
ConsequenceTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders: ConsequenceTB class.
ConsequenceTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
ConsequenceVariantIdKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators: ConsequenceVariantIdKeyCreator class.
ConsequenceVariantIdKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ConsequenceVariantIdKeyCreator: Constructor for ConsequenceVariantIdKeyCreator.
consolidateRow(List<FeatureList>) - Static method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Given a collection of FeatureLists all with the same row key (and differing timestamps), create a consistent view of the features in the feature set corresponding effectively to the last timestamp
CONST_AT_SIGN - Static variable in class net.sourceforge.solexatools.validation.LoginValidator: Constant CONST_AT_SIGN="@"
constant() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: constant.
Constant - Class in net.sourceforge.solexatools.util: Constant class.
Constant() - Constructor for class net.sourceforge.solexatools.util.Constant
Constants - Class in com.github.seqware.queryengine: Defaults for our Constants are defined here and can be overridden by entries in the ~/.seqware/settings file.
Constants() - Constructor for class com.github.seqware.queryengine.Constants
Constants.Term - Enum in com.github.seqware.queryengine
constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: constraint.
contact - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
contacts - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
containsKey(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: containsKey.
containsKey(String) - Method in interface com.github.seqware.queryengine.model.TagSet: containsKey.
ContextImpl - Class in net.sourceforge.seqware.common: ContextImpl class.
contig - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
contig - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
ContigPosition - Class in net.sourceforge.seqware.queryengine.backend.model: ContigPosition class.
ContigPosition() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.ContigPosition
CONTIGPOSITION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model: Constant CONTIGPOSITION=50
ContigPositionComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators: ContigPositionComparator class.
ContigPositionComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.ContigPositionComparator
ContigPositionKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators: ContigPositionKeyCreator class.
ContigPositionKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ContigPositionKeyCreator: Constructor for ContigPositionKeyCreator.
ContigPositionTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders: ContigPositionTB class.
ContigPositionTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
ControllerUtil - Class in net.sourceforge.solexatools.util: ControllerUtil class.
ControllerUtil() - Constructor for class net.sourceforge.solexatools.util.ControllerUtil
ConvertBAMTranscript2Genome - Class in net.sourceforge.seqware.pipeline.modules.BamFilters: Translate reads mapped to transcripts to genomic coordinates.
ConvertBAMTranscript2Genome() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome
copy(boolean) - Method in interface com.github.seqware.queryengine.model.Atom: Copy constructor, used to generate a shallow copy of a Atom ith potentially a new timestamp and UUID
copy(boolean) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Copy constructor, used to generate a shallow copy of a Atom ith potentially a new timestamp and UUID
copyBundle(String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: copyBundle.
copyBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: copyBundleToS3.
copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: copyInputStream.
copyInputStream(InputStream, OutputStream) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil: copyInputStream.
copyProperty(Object, String, Object) - Method in class net.sourceforge.seqware.common.util.NullBeanUtils
copyToFile(BufferedInputStream, String, int, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Copy reader into output.
copyToFile(BufferedInputStream, String, int, String, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Copy reader into output using Cipher.
count - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
countOfRows(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService: countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService: countOfRows.
countOfRows(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: countOfRows.
countOfRows(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO: countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO: countOfRows.
countOfRows(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate: countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate: countOfRows.
countOfRows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: countOfRows.
countOfRows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: countOfRows.
countOfStatus(Study, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: countOfStatus.
countOfStatus(SequencerRun, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: countOfStatus.
countOfStatus(Study, Workflow, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: countOfStatus.
countOfStatus(Study, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: countOfStatus.
countOfStatus(Study, Workflow, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: countOfStatus.
countOfStatus(SequencerRun, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: countOfStatus.
countOfStatus(Study, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: countOfStatus.
countOfStatus(Study, Workflow, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: countOfStatus.
countOfStatus(SequencerRun, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: countOfStatus.
countOfStatus(Study, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: countOfStatus.
countOfStatus(SequencerRun, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: countOfStatus.
countOfStatus(Study, Workflow, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: countOfStatus.
countOfStatus(SequencerRun, Workflow, String) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: countOfStatus.
Coverage - Class in net.sourceforge.seqware.queryengine.backend.model: Coverage class.
Coverage() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Coverage
coverage - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
COVERAGE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model: Constant COVERAGE=40
CoverageIteratorProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators: CoverageIteratorProcessor class.
CoverageIteratorProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.CoverageIteratorProcessor
CoverageProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors: CoverageProcessor class.
CoverageProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor
CoverageResource - Class in net.sourceforge.seqware.queryengine.webservice.view: CoverageResource class.
CoverageResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CoverageResource
CoveragesResource - Class in net.sourceforge.seqware.queryengine.webservice.view: CoveragesResource class.
CoveragesResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.CoveragesResource
CoverageStatsProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors: CoverageStatsProcessor class.
CoverageStatsProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor
CoverageTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders: CoverageTB class.
CoverageTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
coverageXTranscript - Class in net.sourceforge.seqware.pipeline.modules.qc: To get coverage across transcript plot Underlying script: sw_module_CoverageAcrossTranscript.pl (by Sara Grimm) Necessary programs: perl, path to samtools Input: alignment file (bam) a map file, which is generated by the PrepTranscriptDB module, currently, ~/svnroot/seqware-complete/trunk/seqware-pipeline/data/annotation_reference/hg19_transcripts.hg19.20091027.trmap Expected output: coverage across transcript plot
coverageXTranscript() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript
create(SampleSearch) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl: create.
create(SampleSearch) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService: create.
create(SampleSearch) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate: create.
create(SampleSearch) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO: create.
create() - Static method in class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator: create.
createANALYSIS(AnalysisType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of JAXBElement<AnalysisType>}
createANALYSISSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisSet
createAnalysisType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType
createAnalysisTypeANALYSISATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISATTRIBUTES
createAnalysisTypeANALYSISATTRIBUTESANALYSISATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
createAnalysisTypeANALYSISFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISFILES
createAnalysisTypeANALYSISFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISFILES.FILE
createAnalysisTypeANALYSISLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISLINKS
createAnalysisTypeANALYSISLINKSANALYSISLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
createAnalysisTypeANALYSISLINKSANALYSISLINKXREFLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
createAnalysisTypeANALYSISTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.ANALYSISTYPE
createAnalysisTypePARENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.PARENT
createAnalysisTypePARENTEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.PARENT.EXPERIMENTREF
createAnalysisTypePARENTRUNREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.PARENT.RUNREF
createAnalysisTypePARENTSAMPLEPOOLREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.PARENT.SAMPLEPOOLREF
createAnalysisTypePARENTSAMPLEPOOLREFMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
createAnalysisTypePARENTSAMPLEREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.PARENT.SAMPLEREF
createAnalysisTypePARENTSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of AnalysisType.PARENT.STUDYREF
createBashJob(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
createDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator: createDatabase.
createDatabase() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator: createDatabase.
createDirectoryWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: createDirectoryWithUniqueName.
createEXPERIMENT(ExperimentType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of JAXBElement<ExperimentType>}
createEXPERIMENTSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentSet
createExperimentType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType
createExperimentTypeDESIGN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN
createExperimentTypeDESIGNLIBRARYDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR
createExperimentTypeDESIGNLIBRARYDESCRIPTORLIBRARYLAYOUT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
createExperimentTypeDESIGNLIBRARYDESCRIPTORLIBRARYLAYOUTPAIRED() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
createExperimentTypeDESIGNSAMPLEDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN.SAMPLEDESCRIPTOR
createExperimentTypeDESIGNSPOTDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR
createExperimentTypeDESIGNSPOTDESCRIPTORSPOTDECODESPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
createExperimentTypeDESIGNSPOTDESCRIPTORSPOTDECODESPECREADSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
createExperimentTypeEXPERIMENTATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.EXPERIMENTATTRIBUTES
createExperimentTypeEXPERIMENTATTRIBUTESEXPERIMENTATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
createExperimentTypeEXPERIMENTLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.EXPERIMENTLINKS
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
createExperimentTypeEXPERIMENTLINKSEXPERIMENTLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
createExperimentTypePLATFORM() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PLATFORM
createExperimentTypePLATFORMABISOLID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PLATFORM.ABISOLID
createExperimentTypePLATFORMABISOLIDCOLORMATRIX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
createExperimentTypePLATFORMABISOLIDCOLORMATRIXCOLOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
createExperimentTypePLATFORMHELICOS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PLATFORM.HELICOS
createExperimentTypePLATFORMILLUMINA() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PLATFORM.ILLUMINA
createExperimentTypePLATFORMLS454() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PLATFORM.LS454
createExperimentTypePROCESSING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PROCESSING
createExperimentTypePROCESSINGBASECALLS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PROCESSING.BASECALLS
createExperimentTypePROCESSINGQUALITYSCORES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.PROCESSING.QUALITYSCORES
createExperimentTypeSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of ExperimentType.STUDYREF
createFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: create a sqwfile
createFileWithUniqueName(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: createFileWithUniqueName.
createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication: Creates a root Restlet that will receive all incoming calls.
createInboundRoot() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion: Creates a root Restlet that will receive all incoming calls.
createINI(HashMap<String, String>) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager: createINI.
createJavaJob(String, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
createJavaSeqwareModuleJob(String, String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
createKey(Atom) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage: createKey.
createKey(SGID) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage: createKey.
createKey(SGID, boolean) - Static method in class com.github.seqware.queryengine.impl.NonPersistentStorage: createKey.
createPerlJob(String, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
createRUN(RunType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of JAXBElement<RunType>}
createRUNSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunSet
createRunType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType
createRunTypeDATABLOCK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.DATABLOCK
createRunTypeDATABLOCKFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.DATABLOCK.FILES
createRunTypeDATABLOCKFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.DATABLOCK.FILES.FILE
createRunTypeEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.EXPERIMENTREF
createRunTypeRUNATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.RUNATTRIBUTES
createRunTypeRUNATTRIBUTESRUNATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.RUNATTRIBUTES.RUNATTRIBUTE
createRunTypeRUNLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.RUNLINKS
createRunTypeRUNLINKSRUNLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.RUNLINKS.RUNLINK
createRunTypeRUNLINKSRUNLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.RUNLINKS.RUNLINK.ENTREZLINK
createRunTypeRUNLINKSRUNLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of RunType.RUNLINKS.RUNLINK.URLLINK
createSAMPLE(SampleType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of JAXBElement<SampleType>}
createSAMPLESET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleSet
createSampleType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType
createSampleTypeMEMBERS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.MEMBERS
createSampleTypeMEMBERSMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.MEMBERS.MEMBER
createSampleTypeSAMPLEATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.SAMPLEATTRIBUTES
createSampleTypeSAMPLEATTRIBUTESSAMPLEATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
createSampleTypeSAMPLELINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.SAMPLELINKS
createSampleTypeSAMPLELINKSSAMPLELINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.SAMPLELINKS.SAMPLELINK
createSampleTypeSAMPLELINKSSAMPLELINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
createSampleTypeSAMPLELINKSSAMPLELINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
createSampleTypeSAMPLENAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SampleType.SAMPLENAME
createSecondaryKey(SecondaryDatabase, DatabaseEntry, DatabaseEntry, DatabaseEntry) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ConsequenceVariantIdKeyCreator
createSecondaryKey(SecondaryDatabase, DatabaseEntry, DatabaseEntry, DatabaseEntry) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.ContigPositionKeyCreator
createSecondaryKeys(SecondaryDatabase, DatabaseEntry, DatabaseEntry, Set) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyCreator
createSecondaryKeys(SecondaryDatabase, DatabaseEntry, DatabaseEntry, Set) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyOnlyCreator
createSTUDY(StudyType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of JAXBElement<StudyType>}
createSTUDYSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudySet
createStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType
createStudyTypeDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.DESCRIPTOR
createStudyTypeDESCRIPTORSTUDYABSTRACT(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of JAXBElement<String>}
createStudyTypeDESCRIPTORSTUDYTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.DESCRIPTOR.STUDYTYPE
createStudyTypeSTUDYATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.STUDYATTRIBUTES
createStudyTypeSTUDYATTRIBUTESSTUDYATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
createStudyTypeSTUDYLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.STUDYLINKS
createStudyTypeSTUDYLINKSSTUDYLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.STUDYLINKS.STUDYLINK
createStudyTypeSTUDYLINKSSTUDYLINKENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
createStudyTypeSTUDYLINKSSTUDYLINKURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of StudyType.STUDYLINKS.STUDYLINK.URLLINK
createSUBMISSION(SubmissionType) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of JAXBElement<SubmissionType>}
createSUBMISSIONSET() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionSet
createSubmissionType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType
createSubmissionTypeACTIONS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS
createSubmissionTypeACTIONSACTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS.ACTION
createSubmissionTypeACTIONSACTIONADD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS.ACTION.ADD
createSubmissionTypeACTIONSACTIONHOLD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS.ACTION.HOLD
createSubmissionTypeACTIONSACTIONMODIFY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS.ACTION.MODIFY
createSubmissionTypeACTIONSACTIONRELEASE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS.ACTION.RELEASE
createSubmissionTypeACTIONSACTIONSUPPRESS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS.ACTION.SUPPRESS
createSubmissionTypeACTIONSACTIONVALIDATE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.ACTIONS.ACTION.VALIDATE
createSubmissionTypeCONTACTS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.CONTACTS
createSubmissionTypeCONTACTSCONTACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.CONTACTS.CONTACT
createSubmissionTypeFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.FILES
createSubmissionTypeFILESFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create an instance of SubmissionType.FILES.FILE
createSubmittableJob(Configuration, String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest: Sets up the actual job.
createSubmittableJob(Configuration, String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2: Sets up the actual job.
createSymlink(String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Creates symlink of input to output.
createTargetDirectory(String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Creates abstract pathname.
createTargetPath(String, String, String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Creates abstract pathname.
createTempDirectory(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: createTempDirectory.
CreateUpdateManager - Interface in com.github.seqware.queryengine.factory: A very simple Manager that is somewhat like a very stripped down EntityManager from JPA allowing us to create Models and persist them, in other words this handles Create and Update operations out of the basic CRUD operations.
CreateUpdateManager.State - Enum in com.github.seqware.queryengine.factory: This manager defines Atoms to be in the following states
CreateVariantDB - Class in net.sourceforge.seqware.pipeline.modules.queryengine: Purpose: This module serves to create a variant database from the SeqWare Query Engine project that contains SNVs, small indels, and coverage.
CreateVariantDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB
createWorkflow() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant CSV_TYPE="csvtype"
CSV_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Constant CSV_TYPE="csvtype"
currGenomeTagIndexTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
currStep - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
currStep - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
CursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: CursorIterator class.
CursorIterator(Cursor, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: Constructor for CursorIterator.
CustomIntegerEditor - Class in net.sourceforge.solexatools.validation: CustomIntegerEditor class.
CustomIntegerEditor() - Constructor for class net.sourceforge.solexatools.validation.CustomIntegerEditor: Constructor for CustomIntegerEditor.
CycleChecker - Class in net.sourceforge.seqware.pipeline.plugins: CycleChecker class.
CycleChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.CycleChecker: Constructor for CycleChecker.
CycleCheckResource - Class in net.sourceforge.seqware.webservice.resources.queries: CycleCheckResource class.
CycleCheckResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource: Constructor for CycleCheckResource.
cyclecoord - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
cyclecount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
cyclecount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
cyclesequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA

D

data - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
DatabaseCreator - Class in net.sourceforge.seqware.common.util.testtools: DatabaseCreator class.
DatabaseCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.DatabaseCreator
DatabaseIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: DatabaseIDResource class.
DatabaseIDResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource: Constructor for DatabaseIDResource.
DatabaseResource - Class in net.sourceforge.seqware.webservice.resources.tables: DatabaseResource class.
DatabaseResource(String) - Constructor for class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource: Constructor for DatabaseResource.
datablock - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
dataDecryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
dataEncryptionKey - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
dataEncryptionKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
dataSource() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig: dataSource.
DATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
DATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
Daxgenerator - Class in net.sourceforge.seqware.pipeline.daxgenerator: Daxgenerator class.
Daxgenerator() - Constructor for class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator
DaxgeneratorV2 - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
DaxgeneratorV2() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.DaxgeneratorV2
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
db - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
DB_CONN_STRING - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
DB_NAME - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
DB_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
DB_SERVER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
DB_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
DBAccess - Class in net.sourceforge.seqware.common.factory: DBAccess class.
DBCOULDNOTDISCONNECT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant DBCOULDNOTDISCONNECT=81
DBCOULDNOTINITIALIZE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant DBCOULDNOTINITIALIZE=80
DEBUG - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage: Constant DEBUG=true
debug(Object) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.debug(Object).
debug(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.debug(Object,Throwable).
debug - Variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
Debug - Class in net.sourceforge.solexatools: Debug class.
Debug() - Constructor for class net.sourceforge.solexatools.Debug
Decider - Class in net.sourceforge.seqware.pipeline.decider: Abstract Decider class.
Decider() - Constructor for class net.sourceforge.seqware.pipeline.decider.Decider: Notes: Things I would like taken care of for me: * all params in a hash (from both DB and ini file provided) * a list of hashmap that represent a filtered list of files by sample, study, experiment, workflow, etc * a list of files that represent the output from this workflow * a hash that joins the output of this workflow to their parents * the master list of results should be configurable, either to have all the processing events removed where this workflow has already been run or to include these
DeciderInterface - Interface in net.sourceforge.seqware.pipeline.decider: DeciderInterface interface.
DefaultConfig - Class in net.sourceforge.seqware.pipeline.runner: Default Configuation class.
DefaultConfig() - Constructor for class net.sourceforge.seqware.pipeline.runner.DefaultConfig
delete(Experiment, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: delete.
delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: delete.
delete(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService: delete.
delete(File, String) - Method in interface net.sourceforge.seqware.common.business.FileService: delete.
delete(Experiment, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: delete.
delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: delete.
delete(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl: delete.
delete(File, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: delete.
delete(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: delete.
delete(IUS, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: delete.
delete(Lane, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: delete.
delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl: delete.
delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl: delete.
delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl: delete.
delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl: delete.
delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl: delete.
delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl: delete.
delete(Processing, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: delete.
delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl: delete.
delete(Sample, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: delete.
delete(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: delete.
delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: delete.
delete(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: delete.
delete(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: delete.
delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: delete.
delete(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: delete.
delete(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: delete.
delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: delete.
delete(Study, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: delete.
delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: delete.
delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: delete.
delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: delete.
delete(WorkflowRun, String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: delete.
delete(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: delete.
delete(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: delete.
delete(IUS, String) - Method in interface net.sourceforge.seqware.common.business.IUSService: delete.
delete(Lane, String) - Method in interface net.sourceforge.seqware.common.business.LaneService: delete.
delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService: delete.
delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService: delete.
delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService: delete.
delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService: delete.
delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService: delete.
delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService: delete.
delete(Processing, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: delete.
delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService: delete.
delete(Sample, String) - Method in interface net.sourceforge.seqware.common.business.SampleService: delete.
delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: delete.
delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: delete.
delete(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: delete.
delete(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: delete.
delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: delete.
delete(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: delete.
delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: delete.
delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: delete.
delete(Study, String) - Method in interface net.sourceforge.seqware.common.business.StudyService: delete.
delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: delete.
delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: delete.
delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: delete.
delete(WorkflowRun, String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: delete.
delete(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: delete.
delete(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO: delete.
delete(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: delete.
delete(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO: delete.
delete(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO: delete.
delete(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO: delete.
delete(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: delete.
delete(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate: delete.
delete(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: delete.
delete(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate: delete.
delete(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate: delete.
delete(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate: delete.
delete(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: delete.
delete(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: delete.
delete(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate: delete.
delete(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: delete.
delete(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO: delete.
delete(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate: delete.
delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO: delete.
delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate: delete.
delete(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: delete.
delete(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: delete.
delete(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO: delete.
delete(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate: delete.
delete(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate: delete.
delete(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: delete.
delete(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate: delete.
delete(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate: delete.
delete(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate: delete.
delete(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate: delete.
delete(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate: delete.
delete(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate: delete.
delete(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate: delete.
delete(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate: delete.
delete(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: delete.
delete(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate: delete.
delete(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: delete.
delete(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: delete.
delete(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: delete.
delete(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: delete.
delete(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: delete.
delete(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: delete.
delete(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: delete.
delete(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: delete.
delete(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate: delete.
delete(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: delete.
delete(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate: delete.
delete(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate: delete.
delete(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: delete.
delete(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: delete.
delete(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: delete.
delete(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate: delete.
delete(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: delete.
delete(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: delete.
delete(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: delete.
delete(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO: delete.
delete(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: delete.
delete(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: delete.
delete(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: delete.
delete(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO: delete.
delete(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: delete.
delete(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO: delete.
delete(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO: delete.
delete(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO: delete.
delete(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO: delete.
delete(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO: delete.
delete(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO: delete.
delete(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO: delete.
delete(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO: delete.
delete(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: delete.
delete(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO: delete.
delete(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: delete.
delete(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: delete.
delete(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: delete.
delete(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: delete.
delete(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: delete.
delete(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: delete.
delete(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO: delete.
delete(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: delete.
delete(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO: delete.
delete(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: delete.
delete(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO: delete.
delete(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO: delete.
delete(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: delete.
delete(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: delete.
delete(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: delete.
delete(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO: delete.
delete(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: delete.
delete(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: delete.
delete() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
delete() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
delete() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
deleteAll(List<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService: deleteAll.
deleteAll(List<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: deleteAll.
deleteAll(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: deleteAll.
deleteAll(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: deleteAll.
deleteAllWithFolderStore(List<File>) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: deleteAllWithFolderStore.
deleteAllWithFolderStore(List<File>) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: deleteAllWithFolderStore.
deleteAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource: deleteAttribute.
deleteAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource: deleteAttribute.
deleteDirectoryRecursive(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: deleteDirectoryRecursive.
DeleteLoadedIndexPageController - Class in net.sourceforge.solexatools.webapp.controller: DeleteLoadedIndexPageController class.
DeleteLoadedIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController: Constructor for DeleteLoadedIndexPageController.
DeleteTempFile(Registration) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController: DeleteTempFile.
DELETION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant DELETION=3
denovoassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
describeInterfaceAndImplementation(Object, String) - Static method in class net.sourceforge.solexatools.Debug: describeInterfaceAndImplementation.
description - Variable in class net.sourceforge.seqware.common.module.ReturnValue
description - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
description - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
DESCRIPTION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
descriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.ApacheSerialization: Given an array of bytes, get back an atom
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.KryoSerialization: Given an array of bytes, get back an atom
deserialize(byte[], Class<T>) - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization: Given an array of bytes, get back an atom
deserialize(byte[], Class<T>) - Method in interface com.github.seqware.queryengine.impl.SerializationInterface: Given an array of bytes, get back an atom
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtom(SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Generically get back a Atom from the store using a sgid
deserializeTargetToAtom(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToAtoms(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Generically get back a specific class of Atom from the store using a sgid
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
deserializeTargetToLatestAtom(SGID) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Generically get back the latest Atom in a chain from the store using a sgid while ignoring the timestamp
deserializeTargetToLatestAtom(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Generically get back a specific class of Atom from the store using a sgid while ignoring the timestamp to get the latest one
design - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
designdescription - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
destSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper: the feature set that we will be writing to, may be null
dfa14 - Variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer
dibase - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
directBIMap - Variable in class com.github.seqware.queryengine.impl.StorageInterface: These tables are always created with the same names
DIRECTORYNOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant DIRECTORYNOTREADABLE=3
DIRECTORYNOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant DIRECTORYNOTWRITABLE=11
dirPathExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: dirPathExistsAndReadable.
dirPathExistsAndWritable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: dirPathExistsAndWritable.
dissociateTag(Tag) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Remove a new tag from a subject
dissociateTag(Tag) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable: Remove a new tag from a subject
dissociateTag(Tag) - Method in class com.github.seqware.queryengine.model.Tag: Remove a new tag from a subject
do_run() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
do_run() - Method in class net.sourceforge.seqware.pipeline.module.Module: do_run.
do_run() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Performs the main tasks for the module.
do_run() - Method in class net.sourceforge.seqware.pipeline.module.TestModule: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.Picard: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: do_run.
do_run() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: do_run.
do_run() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter: Performs the main tasks for the plugin.
do_run() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker: Performs the main tasks for the plugin.
do_summary() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Just returns a summary of what would be run.
do_summary() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
do_test() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
do_test() - Method in class net.sourceforge.seqware.pipeline.module.Module: do_test.
do_test() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.module.TestModule: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.Picard: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: do_test.
do_test() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: do_test.
do_test() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter: Perform any active system testing here.
do_test() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker: Perform any active system testing here.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.Module: do_verify_input.
do_verify_input() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Input data validation code goes here.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.module.TestModule: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.Picard: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: do_verify_input.
do_verify_input() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: do_verify_input.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.Module: do_verify_output.
do_verify_output() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Perform post-task tests here.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.module.TestModule: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.Picard: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: do_verify_output.
do_verify_output() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: do_verify_output.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.Module: do_verify_parameters.
do_verify_parameters() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Parameter validation code goes here.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.module.TestModule: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.Picard: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: do_verify_parameters.
do_verify_parameters() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: do_verify_parameters.
doCreateTableJson(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: doCreateTableJson.
doInit() - Method in class net.sourceforge.seqware.webservice.resources.BasicResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
doInit() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
doInit() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource
doRetrieveListElements(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: doRetrieveListElements.
doRun() - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect: doRun.
doRun() - Method in class net.sourceforge.seqware.pipeline.runner.RedirectAspect: doRun.
doSetupReport(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController: doSetupReport.
DownloaderController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
DownloaderController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloaderController: Constructor for DownloaderController.
DownloadFileListController - Class in net.sourceforge.solexatools.webapp.controller: DownloadFileListController class.
DownloadFileListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Constructor for DownloadFileListController.
dqc - Class in net.sourceforge.seqware.pipeline.modules.qc: Purpose: This module generates pre and post alignment QC reports using dqc from the DNAA package.
dqc() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.dqc
dropDatabase() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator: dropDatabase.
dropDatabase() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator: dropDatabase.
Dtos - Class in net.sourceforge.seqware.webservice.dto: Methods to convert between domain objects and dtos.
Dtos() - Constructor for class net.sourceforge.seqware.webservice.dto.Dtos
DumpVariantDB - Class in net.sourceforge.seqware.pipeline.modules.queryengine: Purpose: This module takes a BerkeleyDB SeqWare Query Engine database and dumps the variants as a series of BED files, one per contig.
DumpVariantDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB
dumpVCFFromFeatureSetID(FeatureSet, String) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper: dumpVCFFromFeatureSetID.

E

echo - Class in net.sourceforge.seqware.pipeline.modules.examples: echo class.
echo() - Constructor for class net.sourceforge.seqware.pipeline.modules.examples.echo
EMAILADDRESS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
END_ALL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant END_ALL_QUERYDATELONG="end-ALL_query-date-long"
END_PMC_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant END_PMC_QUERYDATELONG="end-PMC_query-date-long"
END_QUAL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant END_QUAL_QUERYDATELONG="end-QUAL_query-date-long"
EntityController - Class in net.sourceforge.solexatools.webapp.controller: The controller.
EntityController() - Constructor for class net.sourceforge.solexatools.webapp.controller.EntityController: Constructor for EntityController.
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
entrezlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
entryToObject(TupleInput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
entryToObject(TupleInput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
entryToObject(TupleInput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
Environment - Class in net.sourceforge.seqware.pipeline.workflowV2.model
Environment() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
EnvUtil - Class in net.sourceforge.seqware.queryengine.webservice.util: EnvUtil class.
EnvUtil() - Constructor for class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil
ENVVARNOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant ENVVARNOTFOUND=14
EOF - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant EOF=-1
EOF - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant EOF=-1
EQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant EQUALS=9
EQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant EQUALS=9
equals(Object) - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
equals(Object) - Method in class com.github.seqware.queryengine.model.Feature
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.FeatureList
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup: Override the equals method for Group, kind of a cheat With other objects we take into account things like version or SGID However, with Group, the object is embedded inside the ACL for other objects explicitly, so the version changes too often for easy API use
equals(Object) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
equals(Object) - Method in class com.github.seqware.queryengine.model.Tag
equals(Object) - Method in class com.github.seqware.queryengine.model.User
equals(Object) - Method in class com.github.seqware.queryengine.util.LazyReference
equals(Object) - Method in class com.github.seqware.queryengine.util.SGID
equals(Object) - Method in class net.sourceforge.seqware.common.model.Expense
equals(Object) - Method in class net.sourceforge.seqware.common.model.Experiment
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign
equals(Object) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
equals(Object) - Method in class net.sourceforge.seqware.common.model.File
equals(Object) - Method in class net.sourceforge.seqware.common.model.FileType
equals(Object) - Method in class net.sourceforge.seqware.common.model.Invoice
equals(Object) - Method in class net.sourceforge.seqware.common.model.IUS
equals(Object) - Method in class net.sourceforge.seqware.common.model.Lane
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySelection
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibrarySource
equals(Object) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
equals(Object) - Method in class net.sourceforge.seqware.common.model.Organism
equals(Object) - Method in class net.sourceforge.seqware.common.model.Platform
equals(Object) - Method in class net.sourceforge.seqware.common.model.Processing
equals(Object) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.Project
equals(Object) - Method in class net.sourceforge.seqware.common.model.Registration
equals(Object) - Method in class net.sourceforge.seqware.common.model.Sample
equals(Object) - Method in class net.sourceforge.seqware.common.model.SampleAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRun
equals(Object) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareStudy
equals(Object) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
equals(Object) - Method in class net.sourceforge.seqware.common.model.Study
equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyAttribute
equals(Object) - Method in class net.sourceforge.seqware.common.model.StudyType
equals(Object) - Method in class net.sourceforge.seqware.common.model.Workflow
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParam
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRun
equals(Object) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
equals(Object) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
error(Object) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.error(Object).
error(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.error(Object,Throwable).
evaluate() - Method in class com.github.seqware.queryengine.kernel.RPNStack: RPN evaluation.
evaluateReturn(Module, String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner: evaluateReturn.
evict(Object) - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions: evict.
ExceptionTools - Class in net.sourceforge.seqware.common.util.exceptiontools: ExceptionTools class.
ExceptionTools() - Constructor for class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools
executeQuery(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: executeQuery.
executeUpdate(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: executeUpdate.
existingStudyType - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
existsExperiment(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
existsIUS(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
existsLane(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
existsProcessing(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
existsSample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
existsSequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
existsStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
EXIT_CODE_EXISTING_NAME - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter: Constant EXIT_CODE_EXISTING_NAME=5
EXIT_CODE_INVALID_ARGS - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter: Constant EXIT_CODE_INVALID_ARGS=1
EXIT_CODE_INVALID_FILE - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter: Constant EXIT_CODE_INVALID_FILE=10
ExitException - Exception in net.sourceforge.seqware.common.util: Created by IntelliJ IDEA.
ExitException(int) - Constructor for exception net.sourceforge.seqware.common.util.ExitException: Constructor for ExitException.
exitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue
ExonCountsRPKM - Class in net.sourceforge.seqware.pipeline.modules.quantification: Calculate base counts, coverage, & RPKM per exon given a BAM file of aligned reads and a list of exons.
ExonCountsRPKM() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM
expectedbasecall - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
expectedNumberReads - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
expectedNumberRuns - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
expectedNumberSpots - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
Expense - Class in net.sourceforge.seqware.common.model: Expense class.
Expense() - Constructor for class net.sourceforge.seqware.common.model.Expense: Constructor for Expense.
Experiment - Class in net.sourceforge.seqware.common.model
Experiment() - Constructor for class net.sourceforge.seqware.common.model.Experiment: Constructor for Experiment.
experiment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
EXPERIMENT_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant EXPERIMENT_ATTRIBUTES="Header.EXPERIMENT_ATTRIBUTES.getTitle()"
EXPERIMENT_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant EXPERIMENT_NAME="Header.EXPERIMENT_NAME.getTitle()"
EXPERIMENT_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant EXPERIMENT_PREFIX="exp_"
EXPERIMENT_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant EXPERIMENT_SWA="Header.EXPERIMENT_SWA.getTitle()"
EXPERIMENT_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant EXPERIMENT_TAG_PREFIX="Header.EXPERIMENT_TAG_PREFIX.getTitle()"
ExperimentAttribute - Class in net.sourceforge.seqware.common.model: ExperimentAttribute generated by hbm2java
ExperimentAttribute() - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute: Constructor for ExperimentAttribute.
ExperimentAttribute(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute: Constructor for ExperimentAttribute.
ExperimentAttribute(int, Experiment, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentAttribute: Constructor for ExperimentAttribute.
experimentattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
ExperimentAttributeDAO - Interface in net.sourceforge.seqware.common.dao: ExperimentAttributeDAO interface.
ExperimentAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ExperimentAttributeDAOHibernate class.
ExperimentAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate
experimentattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
ExperimentController - Class in net.sourceforge.solexatools.webapp.controller: ExperimentController
ExperimentController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController: Constructor for ExperimentController.
ExperimentController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentController: Constructor for ExperimentController.
ExperimentDAO - Interface in net.sourceforge.seqware.common.dao: ExperimentDAO interface.
ExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ExperimentDAOHibernate class.
ExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: Constructor for ExperimentDAOHibernate.
ExperimentIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters: ExperimentIDFilter class.
ExperimentIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter
ExperimentIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentIDResource class.
ExperimentIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource: Constructor for ExperimentIDResource.
ExperimentLibraryDesign - Class in net.sourceforge.seqware.common.model: ExperimentLibraryDesign class.
ExperimentLibraryDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Constructor for ExperimentLibraryDesign.
ExperimentLibraryDesignDAO - Interface in net.sourceforge.seqware.common.dao: ExperimentLibraryDesignDAO interface.
ExperimentLibraryDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ExperimentLibraryDesignDAOHibernate class.
ExperimentLibraryDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate: Constructor for ExperimentLibraryDesignDAOHibernate.
ExperimentLibraryDesignService - Interface in net.sourceforge.seqware.common.business: ExperimentLibraryDesignService interface.
ExperimentLibraryDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ExperimentLibraryDesignServiceImpl class.
ExperimentLibraryDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: Constructor for ExperimentLibraryDesignServiceImpl.
ExperimentLink - Class in net.sourceforge.seqware.common.model: ExperimentLink generated by hbm2java
ExperimentLink() - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink: Constructor for ExperimentLink.
ExperimentLink(int, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink: Constructor for ExperimentLink.
ExperimentLink(int, Experiment, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ExperimentLink: Constructor for ExperimentLink.
experimentlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
ExperimentLinkDAO - Interface in net.sourceforge.seqware.common.dao: ExperimentLinkDAO interface.
ExperimentLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ExperimentLinkDAOHibernate class.
ExperimentLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate
experimentlinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
ExperimentList - Class in net.sourceforge.seqware.common.model.lists: ExperimentList class.
ExperimentList() - Constructor for class net.sourceforge.seqware.common.model.lists.ExperimentList: Constructor for ExperimentList.
experimentref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
experimentref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
ExperimentResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentResource class.
ExperimentResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource: Constructor for ExperimentResource.
ExperimentService - Interface in net.sourceforge.seqware.common.business: ExperimentService interface.
ExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ExperimentServiceImpl class.
ExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: Constructor for ExperimentServiceImpl.
ExperimentSet - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet
ExperimentSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
ExperimentSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Constructor for ExperimentSetupController.
ExperimentSpotDesign - Class in net.sourceforge.seqware.common.model: ExperimentSpotDesign class.
ExperimentSpotDesign() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Constructor for ExperimentSpotDesign.
ExperimentSpotDesignDAO - Interface in net.sourceforge.seqware.common.dao: ExperimentSpotDesignDAO interface.
ExperimentSpotDesignDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ExperimentSpotDesignDAOHibernate class.
ExperimentSpotDesignDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate: Constructor for ExperimentSpotDesignDAOHibernate.
ExperimentSpotDesignReadSpec - Class in net.sourceforge.seqware.common.model: ExperimentSpotDesignReadSpec class.
ExperimentSpotDesignReadSpec() - Constructor for class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Constructor for ExperimentSpotDesignReadSpec.
ExperimentSpotDesignReadSpecComparator - Class in net.sourceforge.seqware.common.model.comparator: ExperimentSpotDesignReadSpecComparator class.
ExperimentSpotDesignReadSpecComparator() - Constructor for class net.sourceforge.seqware.common.model.comparator.ExperimentSpotDesignReadSpecComparator
ExperimentSpotDesignReadSpecDAO - Interface in net.sourceforge.seqware.common.dao: ExperimentSpotDesignReadSpecDAO interface.
ExperimentSpotDesignReadSpecDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ExperimentSpotDesignReadSpecDAOHibernate class.
ExperimentSpotDesignReadSpecDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate: Constructor for ExperimentSpotDesignReadSpecDAOHibernate.
ExperimentSpotDesignReadSpecService - Interface in net.sourceforge.seqware.common.business: ExperimentSpotDesignReadSpecService interface.
ExperimentSpotDesignReadSpecServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ExperimentSpotDesignReadSpecServiceImpl class.
ExperimentSpotDesignReadSpecServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: Constructor for ExperimentSpotDesignReadSpecServiceImpl.
ExperimentSpotDesignService - Interface in net.sourceforge.seqware.common.business: ExperimentSpotDesignService interface.
ExperimentSpotDesignServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ExperimentSpotDesignServiceImpl class.
ExperimentSpotDesignServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl: Constructor for ExperimentSpotDesignServiceImpl.
ExperimentType - Class in net.sourceforge.seqware.queryengine.webservice.model: An Experiment specifies of what will be sequenced and how the sequencing will be performed.
ExperimentType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
ExperimentType.DESIGN - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
ExperimentType.DESIGN.LIBRARYDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
ExperimentType.DESIGN.SAMPLEDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN.SAMPLEDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
ExperimentType.EXPERIMENTATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.EXPERIMENTATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
ExperimentType.EXPERIMENTLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
ExperimentType.PLATFORM - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PLATFORM() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
ExperimentType.PLATFORM.ABISOLID - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
ExperimentType.PLATFORM.HELICOS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PLATFORM.HELICOS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
ExperimentType.PLATFORM.ILLUMINA - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PLATFORM.ILLUMINA() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
ExperimentType.PLATFORM.LS454 - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PLATFORM.LS454() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
ExperimentType.PROCESSING - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PROCESSING() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
ExperimentType.PROCESSING.BASECALLS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PROCESSING.BASECALLS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
ExperimentType.PROCESSING.QUALITYSCORES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.PROCESSING.QUALITYSCORES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
ExperimentType.STUDYREF - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
ExperimentType.STUDYREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
ExperimentUpdateValidator - Class in net.sourceforge.solexatools.validation: ExperimentUpdateValidator class.
ExperimentUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentUpdateValidator
ExperimentValidator - Class in net.sourceforge.solexatools.validation: ExperimentValidator class.
ExperimentValidator() - Constructor for class net.sourceforge.solexatools.validation.ExperimentValidator: Constructor for ExperimentValidator.
EXPIRYTIME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
export() - Method in class com.github.seqware.queryengine.system.exporters.VCFDumper: export.
export() - Method in class com.github.seqware.queryengine.tutorial.BrianTest: export.
export() - Method in class com.github.seqware.queryengine.tutorial.GITest: export.
EXT_PARAMETERS - Static variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Constant EXT_PARAMETERS="ext_parameters"
ext_parameters - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper: parameters that will be usable by the user (the writer of the queries)

F

Factory - Class in net.sourceforge.seqware.queryengine.backend.factory: Abstract Factory class.
Factory() - Constructor for class net.sourceforge.seqware.queryengine.backend.factory.Factory
FactoryInterface - Interface in net.sourceforge.seqware.queryengine.backend.factory: FactoryInterface interface.
FAILED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant FAILED="failed"
FAILED - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun: Constant FAILED="failed"
FAILED - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider: Constant FAILED="failed"
FAILED - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin: Constant FAILED="failed"
FAILURE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant FAILURE=15
Fastq(File, String, String, int) - Static method in class net.sourceforge.seqware.common.util.filetools.validate.Validate: Fastq.
fastqConvNum - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
fatal(Object) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.fatal(Object).
fatal(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.fatal(Object,Throwable).
Feature - Class in com.github.seqware.queryengine.model: Features represent a GVF (which is a more generic version of a VCF).
Feature - Class in net.sourceforge.seqware.queryengine.backend.model: Feature class.
Feature() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Feature
feature - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
FEATURE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model: Constant FEATURE=30
Feature.AdditionalAttributeType - Enum in com.github.seqware.queryengine.model
Feature.Builder - Class in com.github.seqware.queryengine.model
Feature.Builder() - Constructor for class com.github.seqware.queryengine.model.Feature.Builder
Feature.Strand - Enum in com.github.seqware.queryengine.model: Strand locations of features.
FEATURE_SET_ID - Static variable in class com.github.seqware.queryengine.system.importers.FeatureImporter: Constant FEATURE_SET_ID="FeatureSetID"
FEATURE_SET_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper: Constant FEATURE_SET_PARAM='f'
FEATURE_SET_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant FEATURE_SET_PARAM='f'
FeatureFilter - Interface in com.github.seqware.queryengine.plugins.inmemory: Interface for matching functions that we can quickly use in both in-memory and M/R plug-ins.
FeatureImporter - Class in com.github.seqware.queryengine.system.importers: Port of the class from the original prototype, adapted to use the new classes in the new API; command-line interface is the older one without support for SO.
FeatureImporter(int) - Constructor for class com.github.seqware.queryengine.system.importers.FeatureImporter: Constructor for FeatureImporter.
FeatureImporter - Class in net.sourceforge.seqware.queryengine.tools.importers: FeatureImporter class.
FeatureImporter(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.FeatureImporter: Constructor for FeatureImporter.
FeatureIO - Class in com.github.seqware.queryengine.impl.protobufIO: FeatureIO class.
FeatureIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureIO
FeatureList - Class in com.github.seqware.queryengine.model.impl: This is an internal atom class, that should never be viewed by the user.
FeatureList() - Constructor for class com.github.seqware.queryengine.model.impl.FeatureList: Constructor for FeatureList.
FeatureList.Builder - Class in com.github.seqware.queryengine.model.impl
FeatureList.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.FeatureList.Builder
FeatureListIO - Class in com.github.seqware.queryengine.impl.protobufIO: FeatureListIO class.
FeatureListIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO
featureNotImplemented() - Static method in class net.sourceforge.seqware.common.module.ReturnValue: featureNotImplemented.
featurePasses(Feature, Object...) - Method in interface com.github.seqware.queryengine.plugins.inmemory.FeatureFilter: featurePasses.
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin.FeaturesAllFilter
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter
featurePasses(Feature, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin.FeaturesByTagFilter
FEATURES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
FEATURES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
FeatureSet - Class in com.github.seqware.queryengine.model: A feature set is a set (ex: collection, bag) of features.
FeatureSet() - Constructor for class com.github.seqware.queryengine.model.FeatureSet: Creates an instance of an anonymous feature set.
FeatureSet.Builder - Class in com.github.seqware.queryengine.model
FeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.FeatureSet.Builder
FEATURESET_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
featureSetID - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
FEATURESETIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
FeatureSetIO - Class in com.github.seqware.queryengine.impl.protobufIO: FeatureSetIO class.
FeatureSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO
featureSets() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference: Get the list of feature sets associated with this reference.
featureSets() - Method in interface com.github.seqware.queryengine.model.Reference: Get the list of feature sets associated with this reference.
FeatureStoreInterface - Interface in net.sourceforge.seqware.queryengine.backend.store: FeatureStoreInterface interface.
FeatureTB - Class in com.github.seqware.queryengine.impl.tuplebinderIO: FeatureTB class.
FeatureTB() - Constructor for class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
FeatureTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders: FeatureTB class.
FeatureTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: Constant FIELDS=2
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: Constant FIELDS=2
FIELDS - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Constant FIELDS=2
fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
fields - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
File - Class in net.sourceforge.seqware.common.model: File class.
File() - Constructor for class net.sourceforge.seqware.common.model.File: Constructor for File.
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
file - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_EXPERIMENT_NAME="f_exp_name"
FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_EXPERIMENT_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_EXPERIMENT_SWID="f_exp_swid"
FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_FILE="f_file"
FILE_FILE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_FILE="f_file"
FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_IUS="f_ius"
FILE_IUS - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_IUS="f_ius"
FILE_IUS_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_IUS_NAME="f_ius_name"
FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_IUS_SWID="f_ius_swid"
FILE_IUS_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_IUS_SWID="f_ius_swid"
FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_IUS_TAG="f_ius_tag"
FILE_IUS_TAG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_IUS_TAG="f_ius_tag"
FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_LANE="f_lane"
FILE_LANE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_LANE="f_lane"
FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_LANE_NAME="f_lane_name"
FILE_LANE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_LANE_NAME="f_lane_name"
FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_NUMBER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_LANE_NUMBER="f_lane_num"
FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_LANE_SWID="f_lane_swid"
FILE_LANE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_LANE_SWID="f_lane_swid"
FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_LIBRARY="f_library"
FILE_LIBRARY - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_LIBRARY="f_library"
FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_META_TYPE="f_file_meta"
FILE_META_TYPE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_META_TYPE="f_file_meta"
FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_PARENT_SAMPLE_NAME="f_sample_name"
FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PARENT_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_PARENT_SAMPLE_SWID="f_sample_swid"
FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_PATH="f_file_path"
FILE_PATH - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_PATH="f_file_path"
FILE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant FILE_PREFIX="fl_"
FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_ALG - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_PROCESSING_ALG="f_processing_alg"
FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_PROCESSING_SWID="f_processing_swid"
FILE_PROCESSING_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_PROCESSING_SWID="f_processing_swid"
FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_RUN_NAME="f_run_name"
FILE_RUN_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_RUN_NAME="f_run_name"
FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_RUN_SWID="f_run_swid"
FILE_RUN_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_RUN_SWID="f_run_swid"
FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_SAMPLE="f_sample"
FILE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_SAMPLE="f_sample"
FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_SAMPLE_NAME="f_child_sample_name"
FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_SAMPLE_SWID="f_child_sample_swid"
FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_SEQUENCER_NAME="f_seqrun_name"
FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_SEQUENCER_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_SEQUENCER_SWID="f_seqrun_swid"
FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_STUDY_SWID="f_study_swid"
FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_STUDY_TITLE="f_study_title"
FILE_STUDY_TITLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_STUDY_TITLE="f_study_title"
FILE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant FILE_SWA="Header.FILE_SWA.getTitle()"
FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_SWID="f_file_swid"
FILE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_SWID="f_file_swid"
FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_TEMPLATE="f_template"
FILE_TEMPLATE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_TEMPLATE="f_template"
FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_TISSUE="f_tissue"
FILE_TISSUE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_TISSUE="f_tissue"
FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_WF_NAME="f_wf_name"
FILE_WF_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_WF_NAME="f_wf_name"
FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_WF_SWID="f_wf_swid"
FILE_WF_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_WF_SWID="f_wf_swid"
FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant FILE_WF_VERSION="f_wf_version"
FILE_WF_VERSION - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant FILE_WF_VERSION="f_wf_version"
FileAttribute - Class in net.sourceforge.seqware.common.model
FileAttribute() - Constructor for class net.sourceforge.seqware.common.model.FileAttribute: Constructor for FileAttribute.
FileAttribute(Integer) - Constructor for class net.sourceforge.seqware.common.model.FileAttribute: Constructor for FileAttribute.
FileAttributeDAO - Interface in net.sourceforge.seqware.common.dao: FileAttributeDAO interface.
FileAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
FileAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate
FileAttributeResource - Interface in net.sourceforge.seqware.webservice.resources.tables: FileAttributeResource interface.
FileAttributeServerResource - Class in net.sourceforge.seqware.webservice.resources.tables: FileAttributeServerResource class.
FileAttributeServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource: Constructor for FileAttributeServerResource.
FileAttributeService - Interface in net.sourceforge.seqware.common.business: FileAttributeService interface.
FileAttributeServiceImpl - Class in net.sourceforge.seqware.common.business.impl
FileAttributeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl
FileAttributesResource - Interface in net.sourceforge.seqware.webservice.resources.tables: FileAttributesResource interface.
FileAttributesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables: FileAttributesServerResource class.
FileAttributesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource: Constructor for FileAttributesServerResource.
FileController - Class in net.sourceforge.solexatools.webapp.controller: LaneController
FileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController: Constructor for FileController.
FileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.FileController: Constructor for FileController.
FileDAO - Interface in net.sourceforge.seqware.common.dao: FileDAO interface.
FileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: FileDAOHibernate class.
FileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: Constructor for FileDAOHibernate.
FileDto - Class in net.sourceforge.seqware.webservice.dto
FileDto() - Constructor for class net.sourceforge.seqware.webservice.dto.FileDto
FILEEMPTY - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant FILEEMPTY=12
fileExistsAndExecutable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: fileExistsAndExecutable.
fileExistsAndNotEmpty(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: fileExistsAndNotEmpty.
fileExistsAndReadable(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: fileExistsAndReadable.
FileFinder - Class in net.sourceforge.solexatools.util: FileFinder class.
FileFinder() - Constructor for class net.sourceforge.solexatools.util.FileFinder: Constructor for FileFinder.
FileFinder(Pattern) - Constructor for class net.sourceforge.solexatools.util.FileFinder: Constructor for FileFinder.
FileIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: FileIDResource class.
FileIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileIDResource: Constructor for FileIDResource.
FileLinker - Class in net.sourceforge.seqware.pipeline.plugins: FileLinker class.
FileLinker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.FileLinker
FileLinkerLine - Class in net.sourceforge.seqware.pipeline.plugins.filelinker
FileLinkerLine() - Constructor for class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
FileLinkerLineException - Exception in net.sourceforge.seqware.pipeline.plugins.filelinker
FileLinkerLineException(String) - Constructor for exception net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLineException
FileLinkerParser - Class in net.sourceforge.seqware.pipeline.plugins.filelinker
FileLinkerParser() - Constructor for class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser
fileLinkReport() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl: Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.
fileLinkReport(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl: Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.
fileLinkReport() - Method in interface net.sourceforge.seqware.common.business.ValidationReportService: Runs the ValidationReportService.fileLinkReport(List) including all files in the SeqWare meta db.
fileLinkReport(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService: Every file must be associated with at least one processing node and this node in turn must be linked (either directly or through a parent) to one of the following: sequencer_run, lane, ius, sample, experiment or study.
FileLinkReportResource - Class in net.sourceforge.seqware.webservice.resources.tables: FileLinkReportResource class.
FileLinkReportResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource: Constructor for FileLinkReportResource.
FileList - Class in net.sourceforge.seqware.common.model.lists: FileList class.
FileList() - Constructor for class net.sourceforge.seqware.common.model.lists.FileList: Constructor for FileList.
FileMetadata - Class in net.sourceforge.seqware.common.module: This is a simple data structure to represent a file and it's metadata.
FileMetadata() - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
FileMetadata(String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
FileMetadata(String, String, String, String) - Constructor for class net.sourceforge.seqware.common.module.FileMetadata
fileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
fileName - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
filename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
FILENOTEXECUTABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant FILENOTEXECUTABLE=10
FILENOTREADABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant FILENOTREADABLE=4
FILENOTWRITABLE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant FILENOTWRITABLE=5
FileReportDAO - Interface in net.sourceforge.seqware.common.dao: FileReportDAO interface.
FileReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: FileReportDAOHibernate class.
FileReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate
FileReportRow - Class in net.sourceforge.seqware.common.model: FileReportRow class.
FileReportRow() - Constructor for class net.sourceforge.seqware.common.model.FileReportRow
FileReportService - Interface in net.sourceforge.seqware.common.business: FileReportService interface.
FileReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl: FileReportServiceImpl class.
FileReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl
FileResource - Class in net.sourceforge.seqware.queryengine.webservice.view: FileResource class.
FileResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.FileResource
FileResource - Class in net.sourceforge.seqware.webservice.resources.tables: FileResource class.
FileResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileResource: Constructor for FileResource.
fileReverseHierarchyDisplay(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl: Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa).
fileReverseHierarchyDisplay(Integer) - Method in interface net.sourceforge.seqware.common.business.ValidationReportService: Produces a text representation of a reverse hierarchy tree starting at a file (indicated by the provided fileSwa).
FileReverseHierarchyDisplayResource - Class in net.sourceforge.seqware.webservice.resources.tables: FileReverseHierarchyDisplayResource class.
FileReverseHierarchyDisplayResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource: Constructor for FileReverseHierarchyDisplayResource.
files - Variable in class net.sourceforge.seqware.common.module.ReturnValue
files - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
files - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
filesArray - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
filesArray - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
FileService - Interface in net.sourceforge.seqware.common.business: FileService interface.
FileServiceImpl - Class in net.sourceforge.seqware.common.business.impl: FileServiceImpl class.
FileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileServiceImpl: Constructor for FileServiceImpl.
FileSetupController - Class in net.sourceforge.solexatools.webapp.controller: FileSetupController class.
FileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.FileSetupController
filesFromExperiment(Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: FIXME: notice processings directly attached to study aren't examined!
filesFromIUS(IUS, Experiment, Sample, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: filesFromIUS.
filesFromLane(Lane, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: filesFromLane.
filesFromSample(Sample, Experiment, Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: filesFromSample.
filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: FIXME: notice processings directly attached to study aren't examined!
filesFromStudy(Study) - Method in class net.sourceforge.seqware.common.hibernate.PropagateOwnership: filesFromStudy.
FileTools - Class in net.sourceforge.seqware.common.util.filetools: FileTools class.
FileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.FileTools
FileType - Class in net.sourceforge.seqware.common.model: FileType class.
FileType() - Constructor for class net.sourceforge.seqware.common.model.FileType: Constructor for FileType.
filetype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE
filetype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
FILETYPE_ALL - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant FILETYPE_ALL="all"
FileTypeDAO - Interface in net.sourceforge.seqware.common.dao: FileTypeDAO interface.
FileTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: FileTypeDAOHibernate class.
FileTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate: Constructor for FileTypeDAOHibernate.
FileTypeService - Interface in net.sourceforge.seqware.common.business: FileTypeService interface.
FileTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl: FileTypeServiceImpl class.
FileTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl: Constructor for FileTypeServiceImpl.
FileUploadService - Interface in net.sourceforge.seqware.common.business: FileUploadService interface.
FileUploadServiceImpl - Class in net.sourceforge.seqware.common.business.impl: FileUploadServiceImpl class.
FileUploadServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Constructor for FileUploadServiceImpl.
FileValidator - Class in net.sourceforge.solexatools.validation: FileValidator class.
FileValidator() - Constructor for class net.sourceforge.solexatools.validation.FileValidator: Constructor for FileValidator.
fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Static method in class net.sourceforge.solexatools.util.ControllerUtil: fillWorkflowProcessingMap.
fillWorkflowProcessingMap(Processing, Map<WorkflowRun, Set<Processing>>) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: fillWorkflowProcessingMap.
filter() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: filter.
filter() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: filter.
filter() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: filter.
FilteredExperimentResource - Class in net.sourceforge.seqware.webservice.resources.filters: FilteredExperimentResource class.
FilteredExperimentResource() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.FilteredExperimentResource
filterFiles() - Method in class net.sourceforge.seqware.pipeline.decider.Decider: filterFiles.
filterInit() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: filterInit.
filterInit() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: filterInit.
filterInit() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: filterInit.
filterReturnValues(List<ReturnValue>, String, String, boolean, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: filterReturnValues.
filterReturnValuesV2(Writer, List<ReturnValue>, String, String, boolean, boolean, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: filterReturnValuesV2.
finalize() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
find(String, Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: find.
find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService: find.
find(String, Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: find.
find(String, Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: find.
findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO: findAll.
findAll(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO: findAll.
findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate: findAll.
findAll(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate: findAll.
findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate: findAll.
findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO: findAll.
findAll(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate: findAll.
findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO: findAll.
findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate: findAll.
findAll(Lane) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO: findAll.
findAll(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate: findAll.
findAll(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate: findAll.
findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate: findAll.
findAll(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate: findAll.
findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate: findAll.
findAll(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate: findAll.
findAll(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO: findAll.
findAll(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO: findAll.
findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO: findAll.
findAll(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO: findAll.
findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO: findAll.
findAll(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO: findAll.
findAll(String) - Method in class net.sourceforge.solexatools.util.FileFinder: findAll.
findAll(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder: findAll.
FindAllTheFiles - Class in net.sourceforge.seqware.common.hibernate: Should only be used for one query and then discarded and re-instantiated.
FindAllTheFiles() - Constructor for class net.sourceforge.seqware.common.hibernate.FindAllTheFiles
FindAllTheFiles.Header - Enum in net.sourceforge.seqware.common.hibernate
findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: findBelongsToStudy.
findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.business.IUSService: findBelongsToStudy.
findBelongsToStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: findBelongsToStudy.
findBelongsToStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: findBelongsToStudy.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.FileService: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findByCriteria.
findByCriteria(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.IUSService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.LaneService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SampleService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findByCriteria.
findByCriteria(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: findByCriteria.
findByCriteria(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: findByCriteria.
findByCriteria(String, boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: findByCriteria.
findByCriteria(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: findByCriteria.
findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: findByEmailAddress.
findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: findByEmailAddress.
findByEmailAddress(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate: findByEmailAddress.
findByEmailAddress(String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO: findByEmailAddress.
findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: findByEmailAddressAndPassword.
findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: findByEmailAddressAndPassword.
findByEmailAddressAndPassword(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate: findByEmailAddressAndPassword.
findByEmailAddressAndPassword(String, String) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO: findByEmailAddressAndPassword.
findByFilePath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: findByFilePath.
findByFilePath(String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: findByFilePath.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.FileTypeService: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: findByID.
findById(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl: findById.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.OrganismService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.PlatformService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProjectService: findByID.
findById(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleSearchService: findById.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findByID.
findById(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate: findById.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: findByID.
findByID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findByID.
findById(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO: findById.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: findByID.
findByID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: findByID.
findByIDOnlyWithRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: findByIDOnlyWithRunningWR.
findByIDOnlyWithRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: findByIDOnlyWithRunningWR.
findByIDWithIUS(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findByIDWithIUS.
findByIDWithIUS(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findByIDWithIUS.
findByIDWithIUSAndRunningWR(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findByIDWithIUSAndRunningWR.
findByIDWithIUSAndRunningWR(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findByIDWithIUSAndRunningWR.
findByIDWithParams(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: findByIDWithParams.
findByIDWithParams(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: findByIDWithParams.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.LaneService: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.ProjectService: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.SampleService: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: findByName.
findByName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: findByName.
findByName(String) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: findByName.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: findByOwnerID.
findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService: findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: findByOwnerID.
findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: findByOwnerID.
findByOwnerId(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: findByOwnerID.
findByOwnerId(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: findByOwnerId.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: findByOwnerID.
findByOwnerID(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: findByOwnerID.
findByPath(String) - Method in interface net.sourceforge.seqware.common.business.FileService: findByPath.
findByPath(String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: findByPath.
findByPath(String) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: findByPath.
findByPath(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: findByPath.
findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl: findByProcessingExperiment.
findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService: findByProcessingExperiment.
findByProcessingExperiment(Processing, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate: findByProcessingExperiment.
findByProcessingExperiment(Processing, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO: findByProcessingExperiment.
findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl: findByProcessingIUS.
findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService: findByProcessingIUS.
findByProcessingIUS(Processing, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate: findByProcessingIUS.
findByProcessingIUS(Processing, IUS) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO: findByProcessingIUS.
findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl: findByProcessingLane.
findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService: findByProcessingLane.
findByProcessingLane(Processing, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate: findByProcessingLane.
findByProcessingLane(Processing, Lane) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO: findByProcessingLane.
findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl: findByProcessings.
findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService: findByProcessings.
findByProcessings(Processing, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate: findByProcessings.
findByProcessings(Processing, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO: findByProcessings.
findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl: findByProcessingSample.
findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService: findByProcessingSample.
findByProcessingSample(Processing, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate: findByProcessingSample.
findByProcessingSample(Processing, Sample) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO: findByProcessingSample.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl: findByProcessingSequencerRun.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService: findByProcessingSequencerRun.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate: findByProcessingSequencerRun.
findByProcessingSequencerRun(Processing, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO: findByProcessingSequencerRun.
findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl: findByProcessingStudy.
findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService: findByProcessingStudy.
findByProcessingStudy(Processing, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate: findByProcessingStudy.
findByProcessingStudy(Processing, Study) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO: findByProcessingStudy.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: findByStudyIdAndRegistrationId.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: findByStudyIdAndRegistrationId.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: findByStudyIdAndRegistrationId.
findByStudyIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO: findByStudyIdAndRegistrationId.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: findBySWAccession.
findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl: Returns library matching given SeqWare Accession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService: findBySWAccession.
findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.business.LibraryService: Returns library matching given SeqWare Accession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: findBySWAccession.
findBySWAccession(Long) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate: Returns library matching given SeqWare Accesssion.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: findBySWAccession.
findBySWAccession(Long) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO: Returns library matching given SeqWare Accesssion.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: findBySWAccession.
findBySWAccession(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: findBySWAccession.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.SampleService: findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.business.StudyService: findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findByTitle.
findByTitle(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findByTitle.
findByTitle(String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: findByTitle.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: findByWorkflowRunIdAndRegistrationId.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: findByWorkflowRunIdAndRegistrationId.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: findByWorkflowRunIdAndRegistrationId.
findByWorkflowRunIdAndRegistrationId(Integer, Integer) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: findByWorkflowRunIdAndRegistrationId.
FindChildUtil - Class in net.sourceforge.solexatools.util: FindChildUtil class.
FindChildUtil() - Constructor for class net.sourceforge.solexatools.util.FindChildUtil
findDirectories(String) - Method in class net.sourceforge.solexatools.util.FileFinder: findDirectories.
findDirectories(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder: findDirectories.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService: findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService: findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService: findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findFiles.
findFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findFiles.
findFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: findFiles.
findFiles(String) - Method in class net.sourceforge.solexatools.util.FileFinder: findFiles.
findFiles(String, String) - Method in class net.sourceforge.solexatools.util.FileFinder: findFiles.
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: findFilesAssociatedWithASample.
findFilesAssociatedWithASample(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: findFilesAssociatedWithASample.
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithASequencerRun(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithASequencerRun(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: findFilesAssociatedWithASequencerRun.
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: findFilesAssociatedWithAStudy.
findFilesAssociatedWithAStudy(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: findFilesAssociatedWithAStudy.
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: findFilesAssociatedWithAStudy.
findFilesAssociatedWithAStudy(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: findFilesAssociatedWithAStudy.
findFirstWorkflowClass(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder: find the first .class in the clazzPath
findFor(Sample, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: findFor.
findFor(Sample) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: findFor.
findFor(Sample, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: findFor.
findFor(Sample) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: findFor.
findIus() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusSearchResource: Locate IUS by sequencer run name, lane number and optionally sample name.
findIus() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource: Locate IUS by sequencer run name, lane number and optionally sample name.
FindRootUtil - Class in net.sourceforge.solexatools.util: FindRootUtil class.
FindRootUtil() - Constructor for class net.sourceforge.solexatools.util.FindRootUtil
findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: findRunsForIUS.
findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: findRunsForIUS.
findRunsForIUS(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: findRunsForIUS.
findRunsForIUS(IUS) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: findRunsForIUS.
findRunsForSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: Find all the workflow runs for the specific sample.
findRunsForSample(Sample) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: Find all the workflow runs for the specific sample.
findValueByID(WorkflowParam, Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: findValueByID.
FINISHED - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun: Constant FINISHED="completed"
finishTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: finishTransaction.
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: finishTransaction.
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: finishTransaction.
finishTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: finishTransaction.
finishTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: finishTransaction.
FIRSTNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: fix_file_paths.
fix_file_paths(String, ArrayList<String>) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: fix_file_paths.
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: fix_file_paths.
fix_file_paths(String, ArrayList<String>) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: fix_file_paths.
Flat2TableTranscriptDB - Class in net.sourceforge.seqware.pipeline.modules.alignment: Given a set reference transcripts in flat files (fasta sequence file & a mapping/assocation file), create & populate database tables in UCSC format.
Flat2TableTranscriptDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB
Flexigrid - Class in net.sourceforge.solexatools.webapp.metamodel: Flexigrid class.
Flexigrid(int, int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Constructor for Flexigrid.
Flexigrid(int) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Constructor for Flexigrid.
Flexigrid() - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Constructor for Flexigrid.
Flexigrid.Cells - Class in net.sourceforge.solexatools.webapp.metamodel
Flexigrid.Cells(List<String>) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
Flexigrid.ColumnModel - Class in net.sourceforge.solexatools.webapp.metamodel
Flexigrid.ColumnModel(String, String, int, boolean, String) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
FLOAT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant FLOAT=10
FLOAT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FLOAT=10
flowcount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
flowcount - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
flowsequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
flowsequence - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
flush() - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Save all managed models to the back-end
flush(boolean) - Method in class com.github.seqware.queryengine.impl.HBaseModelManager: Normally, when doing a flush, we want to maintain the state of objects that
flush() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Save all managed models to the back-end
flush(boolean) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Normally, when doing a flush, we want to maintain the state of objects that
flushObjects(List<Map.Entry<String, SimpleModelManager.AtomStatePair>>) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Flush objects to the back-end giving a working list
FOLLOW_26_in_key_value_function293 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_26_in_key_value_function293
FOLLOW_26_in_three_param_predicate342 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_26_in_three_param_predicate342
FOLLOW_26_in_three_param_predicate346 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_26_in_three_param_predicate346
FOLLOW_26_in_two_param_predicate317 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_26_in_two_param_predicate317
FOLLOW_AND_in_high_precedence_constraint117 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_AND_in_high_precedence_constraint117
FOLLOW_BRACKET_CLOSE_in_key_value_function297 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_CLOSE_in_key_value_function297
FOLLOW_BRACKET_CLOSE_in_nested_constraint145 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_CLOSE_in_nested_constraint145
FOLLOW_BRACKET_CLOSE_in_three_param_predicate350 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_CLOSE_in_three_param_predicate350
FOLLOW_BRACKET_CLOSE_in_two_param_predicate321 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_CLOSE_in_two_param_predicate321
FOLLOW_BRACKET_OPEN_in_key_value_function288 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_OPEN_in_key_value_function288
FOLLOW_BRACKET_OPEN_in_nested_constraint140 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_OPEN_in_nested_constraint140
FOLLOW_BRACKET_OPEN_in_three_param_predicate337 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_OPEN_in_three_param_predicate337
FOLLOW_BRACKET_OPEN_in_two_param_predicate312 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_BRACKET_OPEN_in_two_param_predicate312
FOLLOW_comparison_in_constraint165 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_comparison_in_constraint165
FOLLOW_comparison_in_constraint175 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_comparison_in_constraint175
FOLLOW_constant_in_constraint168 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_constant_in_constraint168
FOLLOW_constant_in_constraint173 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_constant_in_constraint173
FOLLOW_constraint_in_nested_constraint151 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_constraint_in_nested_constraint151
FOLLOW_EOF_in_query78 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_EOF_in_query78
FOLLOW_high_precedence_constraint_in_low_precedence_constraint91 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_high_precedence_constraint_in_low_precedence_constraint91
FOLLOW_high_precedence_constraint_in_low_precedence_constraint98 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_high_precedence_constraint_in_low_precedence_constraint98
FOLLOW_ID_in_identifier200 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_ID_in_identifier200
FOLLOW_identifier_in_constraint163 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_identifier_in_constraint163
FOLLOW_identifier_in_constraint178 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_identifier_in_constraint178
FOLLOW_key_value_function_in_identifier206 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_key_value_function_in_identifier206
FOLLOW_literal_in_constant249 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_constant249
FOLLOW_literal_in_key_value_function291 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_key_value_function291
FOLLOW_literal_in_key_value_function295 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_key_value_function295
FOLLOW_literal_in_three_param_predicate340 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_three_param_predicate340
FOLLOW_literal_in_three_param_predicate344 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_three_param_predicate344
FOLLOW_literal_in_three_param_predicate348 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_three_param_predicate348
FOLLOW_literal_in_two_param_predicate315 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_two_param_predicate315
FOLLOW_literal_in_two_param_predicate319 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_literal_in_two_param_predicate319
FOLLOW_low_precedence_constraint_in_nested_constraint143 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_low_precedence_constraint_in_nested_constraint143
FOLLOW_low_precedence_constraint_in_query75 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_low_precedence_constraint_in_query75
FOLLOW_NAMED_CONSTANT_in_constant254 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_NAMED_CONSTANT_in_constant254
FOLLOW_NAMED_FUNCTION_in_key_value_function285 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_NAMED_FUNCTION_in_key_value_function285
FOLLOW_NAMED_THREE_PARAM_PREDICATE_in_three_param_predicate334 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_NAMED_THREE_PARAM_PREDICATE_in_three_param_predicate334
FOLLOW_NAMED_TWO_PARAM_PREDICATE_in_two_param_predicate309 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_NAMED_TWO_PARAM_PREDICATE_in_two_param_predicate309
FOLLOW_nested_constraint_in_high_precedence_constraint113 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_nested_constraint_in_high_precedence_constraint113
FOLLOW_nested_constraint_in_high_precedence_constraint120 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_nested_constraint_in_high_precedence_constraint120
FOLLOW_NOT_in_nested_constraint135 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_NOT_in_nested_constraint135
FOLLOW_OR_in_low_precedence_constraint95 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_OR_in_low_precedence_constraint95
FOLLOW_three_param_predicate_in_constraint189 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_three_param_predicate_in_constraint189
FOLLOW_two_param_predicate_in_constraint183 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant FOLLOW_two_param_predicate_in_constraint183
FOREVER - Static variable in interface com.github.seqware.queryengine.model.interfaces.TTLable: A time to set that means that the associated object should never expire
forJSON(String) - Static method in class net.sourceforge.seqware.common.util.jsontools.JsonUtil: forJSON.
forJSON(String) - Static method in class net.sourceforge.solexatools.util.ModelUtil: forJSON.
formatCode - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
frame - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
Freemarker - Class in net.sourceforge.seqware.common.util.freemarker: Freemarker class.
Freemarker() - Constructor for class net.sourceforge.seqware.common.util.freemarker.Freemarker
FREEMARKEREXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant FREEMARKEREXCEPTION=70
FRIENDLY_ROWKEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
friendlyRowKey - Variable in class com.github.seqware.queryengine.util.SGID: this can be used to override the randomly generated IDs for the back-end.
fromBaseN(String, int) - Static method in class com.github.seqware.queryengine.kernel.Compression: Returns the integer extracted from the given string in a certain base.
fromDto(AttributeDto, Class<T>) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: fromDto.
fromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowReport: fromWorkflow.
FSGID - Class in com.github.seqware.queryengine.util: Special class for Features which also stores the row key for features.
FSGID(long, long, long, String, String, SGID, boolean) - Constructor for class com.github.seqware.queryengine.util.FSGID: Create a fully functional FSGID given raw data
FSGID(SGID, FSGID) - Constructor for class com.github.seqware.queryengine.util.FSGID: construct a FSGID based on all the components of a SGID while taking the non-unique aspects on a FSGID, used when creating FeatureLists only
FSGID(SGID, Feature, FeatureSet) - Constructor for class com.github.seqware.queryengine.util.FSGID: Create a fully functional FSGID given models from the front-end
FSGIDIO - Class in com.github.seqware.queryengine.impl.protobufIO: FSGIDIO class.
FSGIDIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO
fuzzyStartPositionMax - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
fuzzyStopPositionMin - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant

G

geneChr - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
GeneCountsRPKM - Class in net.sourceforge.seqware.pipeline.modules.quantification: Calculate read counts, coverage, & RPKM per transcript and gene given a BAM file of aligned reads.
GeneCountsRPKM() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM
geneCoverage - Class in net.sourceforge.seqware.pipeline.modules.qc: To get coverage across transcript plot Underlying script: sw_module_CoverageAcrossTranscript.pl (by Sara Grimm) Necessary programs: perl, path to samtools Input: alignment file (bam) a map file, which is generated by the PrepTranscriptDB module, currently, ~/svnroot/seqware-complete/trunk/seqware-pipeline/data/annotation_reference/hg19_transcripts.hg19.20091027.trmap Expected output: coverage across transcript plot
geneCoverage() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage
geneId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
geneId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
generateDax(AbstractWorkflowDataModel, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.DaxgeneratorV2: generate a dax file from the object model
generateDaxFile(WorkflowInfo, File, String, Map<String, String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow: generateDaxFile.
GeneReportResource - Class in net.sourceforge.seqware.queryengine.webservice.view: GeneReportResource class.
GeneReportResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.GeneReportResource
GenericCommandRunner - Class in net.sourceforge.seqware.pipeline.modules: This is a very simple module that takes a few options on the command line and then passes the rest of the arguments to whatever command is specified.
GenericCommandRunner() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner
GenericDBResource - Class in net.sourceforge.seqware.webservice.resources.queries: GenericDBResource class.
GenericDBResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource: Constructor for GenericDBResource.
GenericMetadataSaver - Class in net.sourceforge.seqware.pipeline.modules: This is a very simple module is used to save both a processing event and 0 or more files to the metadb.
GenericMetadataSaver() - Constructor for class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver
GenericQCGenome - Class in net.sourceforge.seqware.pipeline.modules.qc: Estimate % of reads in a given lane that align to a specified set of sequence databases.
GenericQCGenome() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome
GenericTemplateResource - Class in net.sourceforge.seqware.queryengine.webservice.view: GenericTemplateResource class.
GenericTemplateResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
genomeId - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
genomeTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
genomicSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
get() - Method in class com.github.seqware.queryengine.model.Analysis: Blocking call to retrieve results of a query
get() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Blocking call to retrieve results of a query
get(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: get.
get() - Method in interface com.github.seqware.queryengine.model.QueryFuture: Blocking call to retrieve results of a query
get(String) - Method in interface com.github.seqware.queryengine.model.TagSet: get.
get() - Method in class com.github.seqware.queryengine.util.LazyLatestReference: Retrieve the lazy referenced object if possible and return it
get() - Method in class com.github.seqware.queryengine.util.LazyReference: Retrieve the lazy referenced object if possible and return it
get(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService: get.
get(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl: get.
get(File) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO: get.
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO: get.
get(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate: get.
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate: get.
get(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate: get.
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate: get.
get(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate: get.
get(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate: get.
get(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO: get.
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO: get.
get(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO: get.
get(Integer) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO: get.
get() - Static method in class net.sourceforge.seqware.common.factory.DBAccess: get.
get(String, String, boolean) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams: get.
get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
get() - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
get() - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
get() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource
get_description() - Method in class net.sourceforge.seqware.pipeline.decider.Decider: Generates a short description of the plugin, preferably one line.
get_description() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: Generates a short description of the plugin, preferably one line.
get_description() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager: get_description.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: get_description.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner: get_description.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter: Generates a short description of the plugin, preferably one line.
get_description() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker: Generates a short description of the plugin, preferably one line.
get_galaxy_xml() - Method in class net.sourceforge.seqware.pipeline.module.Module: Output Galaxy definition files so you can use this module with Galaxy.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.decider.Decider: Generates a "help" message for the user of the plugin.
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Generates a "help" message for the user of the plugin.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.module.Module: Generates a "help" message for the user of the module.
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.bmfsplit: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.Picard: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: Generates a "help" message for the user of the module.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: get_syntax.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: Generates a "help" message for the user of the plugin.
get_syntax() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Generates a "help" message for the user of the plugin.
get_syntax() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Generates a "help" message for the user of the plugin.
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: get_workflow_info.
get_workflow_info(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: get_workflow_info.
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: get_workflow_info.
get_workflow_info(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: get_workflow_info.
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: get_workflow_run_accession.
get_workflow_run_accession(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: get_workflow_run_accession.
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: get_workflow_run_accession.
get_workflow_run_accession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: get_workflow_run_accession.
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: get_workflow_run_id.
get_workflow_run_id(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: get_workflow_run_id.
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: get_workflow_run_id.
get_workflow_run_id(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: get_workflow_run_id.
getABISOLID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Gets the value of the abisolid property.
getAbstractStr() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field abstractStr.
getABUNDANCEMEASUREMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the abundancemeasurement property.
getAccess() - Method in class com.github.seqware.queryengine.model.interfaces.ACL: Get whether 0) owner can read, 1) owner can write, 2) group can read, 3) group can write, 4) other users can read 5) other users can write
getAccession() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field accession.
getAccession() - Method in class net.sourceforge.seqware.common.model.Organism: Getter for the field accession.
getAccession() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field accession.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Gets the value of the accession property.
getAccession() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the accession property.
getAccessionFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
getAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getAcl() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
getAclBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getAclOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getAclOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getAclOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
getACLs() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getACLs.
getACTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS: Gets the value of the action property.
getACTIONS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the actions property.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareFile: Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareLane: Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareSample: Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareStudy: Getter for the field active.
getActive() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Getter for the field active.
getAdapters() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field adapters.
getAdapterSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field adapterSpec.
getADAPTERSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC: Gets the value of the adapterspec property.
getADD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Gets the value of the add property.
getAddedSurcharge() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field addedSurcharge.
getAdditionalAttribute(String) - Method in class com.github.seqware.queryengine.model.Feature: Returns the value of an additional attribute or null of the attribute does not exist.
getAdditionalAttributeNames() - Method in class com.github.seqware.queryengine.model.Feature: Returns the names of the additional attributes stored.
getAdhoctagset() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field adhoctagset.
getAgent() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field agent.
getAlgo() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: get the job algorithm
getAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field algorithm.
getAlgorithm() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field algorithm.
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.Module: Getter for the field algorithm.
getAlgorithm() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: getAlgorithm.
getAlgorithm() - Method in class net.sourceforge.seqware.pipeline.module.TestModule: Getter for the field algorithm.
getAlias() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field alias.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Gets the value of the alias property.
getAlias() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the alias property.
getAlign() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
getAligners() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: Getter for the field aligners.
getAligners(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: Getter for the field aligners.
getAligners() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: Getter for the field aligners.
getAligners(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: Getter for the field aligners.
getAligners() - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: Getter for the field aligners.
getAligners(int) - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: Getter for the field aligners.
getAll() - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO: getAll.
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate: getAll.
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate: getAll.
getAll() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate: getAll.
getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO: getAll.
getAll() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO: getAll.
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.HBaseStorage: For debugging or very non-optimal implementations
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: For debugging or very non-optimal implementations
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.StorageInterface: For debugging or very non-optimal implementations
getAllAtoms() - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: For debugging or very non-optimal implementations
getAllAtomsForTable(String) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: getAllAtomsForTable.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllFeatureListsForFeatureSet(FeatureSet) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Iterate through all the feature "buckets" in a feature set, this might be moved later.
getAllHtml(Lane, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: getAllHtml.
getAllHtml(IUS, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: getAllHtml.
getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: getAllHtml.
getAllHtml(Processing, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil: getAllHtml.
getAllHtml(IUS, Registration, String, Integer, List<String>, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil: getAllHtml.
getAllHtml(Study, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getAllHtml.
getAllHtml(Experiment, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getAllHtml.
getAllHtml(Sample, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getAllHtml.
getAllHtml(Lane, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getAllHtml.
getAllItems() - Method in class net.sourceforge.solexatools.util.PageInfo: Getter for the field allItems.
getAllProcessing() - Method in class net.sourceforge.seqware.common.model.SequencerRun: getAllProcessing.
getAllProcessings() - Method in class net.sourceforge.seqware.common.model.Lane: getAllProcessings.
getAllRuns() - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport: Find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.
getAllSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: Get all selected Files, the files are organized by the name of the parameter (key) and a list of files selected (value) via a hash.
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getAllStudies.
getAllStudies() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getAllStudies.
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getAllStudies.
getAllStudies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getAllStudies.
getANALYSIS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisSet: Gets the value of the analysis property.
getANALYSISATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES: Gets the value of the analysisattribute property.
getANALYSISATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the analysisattributes property.
getAnalysisCenter() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the analysisCenter property.
getANALYSISFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the analysisfiles property.
getAnalysisIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAnalysisIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getAnalysisIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getAnalysisIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAnalysisIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAnalysisIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAnalysisIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getAnalysisIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getAnalysisIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAnalysisIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getAnalysisIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getAnalysisIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAnalysisIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getAnalysisIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getAnalysisIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAnalysisIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getAnalysisIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getANALYSISLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS: Gets the value of the analysislink property.
getANALYSISLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the analysislinks property.
getAnalysisPlugins() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getAnalysisPlugins.
getAnalysisPlugins() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getAnalysisPlugins.
getAnalysisPlugins() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getAnalysisPlugins.
getAnalysisSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: getAnalysisSets.
getAnalysisSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getAnalysisSets.
getAnalysisSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getAnalysisSets.
getAnalysisSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getAnalysisSets.
getANALYSISTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the analysistype property.
getAnalysisWorkflowHtml(WorkflowRun, Registration, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getAnalysisWorkflowHtml.
getAnonymizedName() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field anonymizedName.
getANONYMIZEDNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME: Gets the value of the anonymizedname property.
getApplication() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
getApplicationInfo(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
getArch() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
getArgs(String) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams: getArgs.
getArgs(String, boolean) - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams: getArgs.
getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
getArguments() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule: Getter for the field arguments.
getAsText() - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor: getAsText.
getAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getAtom() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getAtomBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getAtomBySGID(SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Find a object in the back-end by a globally unique SGID
getAtomBySGID(Class<T>, SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Find an object in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAtomBySGID(SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Deprecated. It is much more efficient to retrieve an Atom when you know the class
getAtomBySGID(Class<T>, SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Find an object in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getAtomOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getAtomOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getAtomsBySGID(Class<T>, SGID...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Find a batch of objects in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAtomsBySGID(Class<T>, SGID...) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Find a batch of objects in the back-end when a specific class is known using a globally unique SGID while taking into account the timestamp
getAttribute(String) - Method in class com.github.seqware.queryengine.model.Feature: Generic implementation for retrieving the value of a GVF or additional attribute.
getAttribute(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: getAttribute.
getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource: Getter for the field attribute.
getAttribute() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource: getAttribute.
getAttribute() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource: getAttribute.
getAttributes() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field attributes.
getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field attributes.
getAttributes() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto: Getter for the field attributes.
getBackEnd() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory: Get a reference to the currently operating back-end
getBackendTimestamp() - Method in class com.github.seqware.queryengine.util.SGID: Getter for the field backendTimestamp.
getBarcode() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field barcode.
getBarcodeSeqence() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER: Gets the value of the barcodeSeqence property.
getBaseCaller() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field baseCaller.
getBASECALLER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS: Gets the value of the basecaller property.
getBASECALLS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING: Gets the value of the basecalls property.
getBaseCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field baseCoord.
getBASECOORD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Gets the value of the basecoord property.
getBaseDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field baseDir.
getBaseIniFile() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field baseIniFile.
getBaseQualities() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field baseQualities.
getBatch_size() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field batch_size.
getBinSize() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field binSize.
getBinSize() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field binSize.
getBlockCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field blockCount.
getBlockSizes() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field blockSizes.
getBlockStarts() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field blockStarts.
getBrokerName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the brokerName property.
getBundleInfo(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: getBundleInfo.
getCacheSize() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field cacheSize.
getCalledBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field calledBase.
getCalledBaseCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field calledBaseCount.
getCalledBaseCountForward() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field calledBaseCountForward.
getCalledBaseCountReverse() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field calledBaseCountReverse.
getCallOne() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field callOne.
getCallTwo() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field callTwo.
getCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getCascade() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
getCascade() - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet: Return whether cascade should occur on deletion
getCascade() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Return whether cascade should occur on deletion
getCascade() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable: Return whether cascade should occur on deletion
getCell() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
getCenterName() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field centerName.
getCenterName() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field centerName.
getCenterName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the centerName property.
getCENTERNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Gets the value of the centername property.
getCenterName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the centerName property.
getCenterProjectName() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field centerProjectName.
getCENTERPROJECTNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Gets the value of the centerprojectname property.
getChecksum() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE: Gets the value of the checksum property.
getChecksumMethod() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE: Gets the value of the checksumMethod property.
getChildMaps() - Method in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
getChildren() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field children.
getChildren() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field children.
getChildren() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
getChildrenUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field childrenUrls.
getChildSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Getter for the field childSample.
getChildSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field childSample.
getChildSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getChildSamples.
getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getChildSamples.
getChildSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getChildSamples.
getChildSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getChildSamples.
getChildTags() - Method in class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
getClassesDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field classesDir.
getClassPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
getClientNotes() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field clientNotes.
getCode() - Method in class net.sourceforge.seqware.common.model.Organism: Getter for the field code.
getCode() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto: Getter for the field code.
getCodingStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field codingStart.
getCodingStop() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field codingStop.
getCOLOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX: Gets the value of the color property.
getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field colorMatrix.
getColorMatrix() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field colorMatrix.
getCOLORMATRIX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Gets the value of the colormatrix property.
getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field colorMatrixCode.
getColorMatrixCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field colorMatrixCode.
getCOLORMATRIXCODE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Gets the value of the colormatrixcode property.
getCommand() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field command.
getCommand() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field command.
getCommand() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field command.
getCommand() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
getCommand() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
getCOMMONNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME: Gets the value of the commonname property.
getCompleted() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field completed.
getCompute() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getComputeReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field computeReq.
getConfigPath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field configPath.
getConfigs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication: Getter for the field configuration.
getConfiguration() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion: Getter for the field configuration.
getConfirmEmailAddress() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO: Getter for the field confirmEmailAddress.
getConfirmPassword() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO: Getter for the field confirmPassword.
getConnectionString() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field connectionString.
getConsensusAveSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field consensusAveSeqQuality.
getConsensusBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field consensusBase.
getConsensusCallQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field consensusCallQuality.
getConsensusMaxSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field consensusMaxSeqQuality.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getConsequence.
getConsequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getConsequence.
getConsequence(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getConsequence.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getConsequencesByMismatch.
getConsequencesByMismatch(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getConsequencesByMismatch.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getConsequencesByTag.
getConsequencesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getConsequencesByTag.
getConsequencesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getConsequencesByTag.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getConsequenceTagsBySearch.
getConsequenceTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getConsequenceTagsBySearch.
getConstructionProtocol() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field constructionProtocol.
getCONTACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS: Gets the value of the contact property.
getCONTACTS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the contacts property.
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition: Getter for the field contig.
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel: Getter for the field contig.
getContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field contig.
getContig() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Getter for the field contig.
getCount() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterable
getCount() - Method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet: Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet: Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.util.InMemoryIterable: Get number of elements in set
getCount() - Method in interface com.github.seqware.queryengine.util.SeqWareIterable: Get number of elements in set
getCount() - Method in class com.github.seqware.queryengine.util.SGIDIterable: Get number of elements in set
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: Getter for the field count.
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: getCount.
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: Not supported for HBase backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: Not supported for HBase backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: Not supported for this backend!
getCount() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: getCount.
getCount() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator: getCount.
getCountFile() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field countFile.
getCountFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: getCountFiles.
getCountFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: getCountFiles.
getCountFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: getCountFiles.
getCountFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: getCountFiles.
getCoverage(Integer) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: Getter for the field coverage.
getCoverage() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: Getter for the field coverage.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getCoverages.
getCoverages(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getCoverages.
getCoverages(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getCoverages.
getCoverages(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getCoverages.
getCoverages(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getCoverages.
getCreated() - Method in class net.sourceforge.seqware.common.model.SampleSearch: Getter for the field created.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field createTimestamp.
getCreateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field createTimestamp.
getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field createTimeStamp.
getCreateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field createTimeStamp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile: Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane: Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Getter for the field createTstmp.
getCreateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample: Getter for the field createTstmp.
getCriteria() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController: Getter for the field criteria.
getCurrentSelectedFiles(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getCurrentSelectedFiles.
getCurrentSelectedNodes(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getCurrentSelectedNodes.
getCurrentWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getCurrentWorkflow.
getCurrentWorkflowParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getCurrentWorkflowParam.
getCurrentWorkingDir() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field currentWorkingDir.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: Getter for the field cursor.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: Not applicable for HBase backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: Not applicable for HBase backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: Not applicable for Postgres backend.
getCursor() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: Getter for the field cursor.
getCursor() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator: getCursor.
getCwd() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field cwd.
getCycleCoord() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field cycleCoord.
getCYCLECOORD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Gets the value of the cyclecoord property.
getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field cycleCount.
getCycleCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field cycleCount.
getCYCLECOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Gets the value of the cyclecount property.
getCYCLECOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA: Gets the value of the cyclecount property.
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field cycleDescriptor.
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field cycleDescriptor.
getCycleDescriptor() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field cycleDescriptor.
getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field cycles.
getCycles() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field cycles.
getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field cycleSequence.
getCycleSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field cycleSequence.
getCYCLESEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA: Gets the value of the cyclesequence property.
getData() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: Getter for the field data.
getDatabase() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field database.
getDATABLOCK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the datablock property.
getDataModel() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine: get the objectModel for the workflow
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getDate() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getDate() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getDax() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field dax.
getDaxDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getDaysUntilDue() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field daysUntilDue.
getDb() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.IUSLink: Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.LaneLink: Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.SampleLink: Getter for the field db.
getDb() - Method in class net.sourceforge.seqware.common.model.StudyLink: Getter for the field db.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK: Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK: Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK: Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK: Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK: Gets the value of the db property.
getDB() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK: Gets the value of the db property.
getDbmd() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Getter for the field dbmd.
getDecodeMethod() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field decodeMethod.
getDecryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Gets cipher by DecryptKey.
getDecryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: getDecryptCipher.
getDefaultDirManagerExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getDefaultInstance() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getDefaultInstanceForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getDefaultJavaExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
getDefaultPerlExcutable(AbstractWorkflowDataModel) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
getDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field defaultValue.
getDelegates() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: getDelegates.
getDelegates() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: getDelegates.
getDENOVOASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the denovoassembly property.
getDependentElement(PegasusJob) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getDescription() - Method in interface com.github.seqware.queryengine.model.AnalysisSet: Get the description associated with this analysisSet
getDescription() - Method in class com.github.seqware.queryengine.model.FeatureSet: Get the description associated with this FeatureSet
getDescription() - Method in interface com.github.seqware.queryengine.model.Group: Get the description associated with this group
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet: Get the description associated with this analysisSet
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Get the description associated with this FeatureSet
getDescription() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup: Get the description associated with this group
getDescription() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Get the description associated with this FeatureSet
getDescription() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySelection: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.LibrarySource: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Platform: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.StudyType: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getDescription() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field description.
getDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the description property.
getDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Gets the value of the description property.
getDescription() - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Getter for the field description.
getDescription() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field description.
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getDescriptor() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getDescriptor() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Gets the value of the descriptor property.
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getDescriptorForType() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getDescriptorForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getDESIGN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the design property.
getDESIGNDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Gets the value of the designdescription property.
getDibase() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR: Gets the value of the dibase property.
getDirContext() - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication: getDirContext.
getDirectories() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getDirectoriesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder: Getter for the field directoriesNumber.
getDirectorySize() - Method in class net.sourceforge.solexatools.util.FileFinder: getDirectorySize.
getDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field display.
getDisplay() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
getDisplayName() - Method in class net.sourceforge.seqware.common.model.FileType: Getter for the field displayName.
getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field displayName.
getDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Getter for the field displayName.
getDisplayName() - Method in class net.sourceforge.solexatools.util.SummaryLine: Getter for the field displayName.
getDisplayValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field displayValue.
getDomainObject() - Method in class net.sourceforge.seqware.common.model.RegistrationDTO: Getter for the field domainObject.
getDomainObject() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO: Getter for the field domainObject.
getEmail() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Getter for the field email.
getEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getEmailAddress() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getEmailAddress() - Method in class com.github.seqware.queryengine.model.User: Get email address
getEmailAddress() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field emailAddress.
getEncryptCipher(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Gets cipher by EncryptKey.
getEncryptCipher() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: getEncryptCipher.
getEnd() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field end.
getEndDate() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field endDate.
getEndPage() - Method in class net.sourceforge.solexatools.util.PageInfo: Getter for the field endPage.
getEntityUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Getter for the field entityUrl.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK: Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK: Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK: Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK: Gets the value of the entrezlink property.
getENTREZLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK: Gets the value of the entrezlink property.
getEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getError() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread: Getter for the field error.
getErrorCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: getErrorCnt.
getErrorCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: getErrorCnt.
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.Lane: getErrorCnt.
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun: getErrorCnt.
getErrorCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: getErrorCnt.
getErrorCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field errorCount.
getExecutionEnv() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getExistingStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE: Gets the value of the existingStudyType property.
getExistingType() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field existingType.
getExistingTypeInt() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field existingTypeInt.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException: getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SeqwareException: getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadFileException: getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwBadModuleException: getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwParameterException: getExitCode.
getExitCode() - Method in exception net.sourceforge.seqware.common.err.SwRunnerParameterException: getExitCode.
getExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field exitStatus.
getExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field exitStatus.
getExpectedBaseCall() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field expectedBaseCall.
getEXPECTEDBASECALL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Gets the value of the expectedbasecall property.
getExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expectedNumberReads.
getExpectedNumberReads() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the expectedNumberReads property.
getExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expectedNumberRuns.
getExpectedNumberRuns() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the expectedNumberRuns property.
getExpectedNumberSpots() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expectedNumberSpots.
getExpectedNumberSpots() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the expectedNumberSpots property.
getExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field expectedNumReads.
getExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field expectedNumRuns.
getExpectedNumSpots() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field expectedNumSpots.
getExpenseId() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field expenseId.
getExpenses() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field expenses.
getExpenseType() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field expenseType.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field experiment.
getExperiment() - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Getter for the field experiment.
getEXPERIMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentSet: Gets the value of the experiment property.
getEXPERIMENTATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES: Gets the value of the experimentattribute property.
getExperimentAttributeId() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Getter for the field experimentAttributeId.
getExperimentAttributes() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field experimentAttributes.
getEXPERIMENTATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the experimentattributes property.
getExperimentHtml(Experiment, Registration, String, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getExperimentHtml.
getExperimentId() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field experimentId.
getExperimentLibraryDesign() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field experimentLibraryDesign.
getExperimentLibraryDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field experimentLibraryDesignId.
getExperimentLibraryDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field experimentLibraryDesignService.
getEXPERIMENTLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS: Gets the value of the experimentlink property.
getExperimentLinkId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Getter for the field experimentLinkId.
getExperimentLinks() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field experimentLinks.
getEXPERIMENTLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the experimentlinks property.
getEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Gets the value of the experimentref property.
getEXPERIMENTREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the experimentref property.
getExperiments() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field experiments.
getExperiments() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field experiments.
getExperimentService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.validation.ExperimentValidator: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field experimentService.
getExperimentService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field experimentService.
getExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getExperimentServiceBean.
getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field experimentSpotDesign.
getExperimentSpotDesign() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field experimentSpotDesign.
getExperimentSpotDesignId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field experimentSpotDesignId.
getExperimentSpotDesignReadSpecId() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field experimentSpotDesignReadSpecId.
getExperimentSpotDesignReadSpecService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field experimentSpotDesignReadSpecService.
getExperimentSpotDesignService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field experimentSpotDesignService.
getExperimentSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getExpiryDate() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Return the expiry date
getExpiryDate() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable: Return the expiry date
getExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
getExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getExpiryTime() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
getExpiryTime() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Return raw expiry time
getExpiryTime() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable: Return raw expiry time
getExpLibDesignDesc() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expLibDesignDesc.
getExpLibDesignName() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expLibDesignName.
getExpLibDesignProtocol() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expLibDesignProtocol.
getExpLibDesignSelection() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expLibDesignSelection.
getExpLibDesignSource() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expLibDesignSource.
getExpLibDesignStrategy() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expLibDesignStrategy.
getExpSpotDesignAdapterSpec() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expSpotDesignAdapterSpec.
getExpSpotDesignReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expSpotDesignReadsPerSpot.
getExpSpotDesignTagSpec() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field expSpotDesignTagSpec.
getExtension() - Method in class net.sourceforge.seqware.common.model.FileType: Getter for the field extension.
getExtension(String) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: getExtension.
getExternalId() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field externalId.
getExternalSerializationVersion() - Method in interface com.github.seqware.queryengine.model.Atom: Get the serializationVersion for this particular atom.
getExternalSerializationVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get the serializationVersion for this particular atom.
getFailed() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field failed.
getFailedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: getFailedCount.
getFailedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: getFailedCount.
getFailedJobsInfo(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools: This method will examine a Pegasus DAX log directory for a given workflow and identify the log files for jobs that failed.
getFastqConvNum() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field fastqConvNum.
getFastqConvNum() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field fastqConvNum.
getFeature() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field feature.
getFeature(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getFeature.
getFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getFeature.
getFeature(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getFeature.
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getFeatures(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getFeatures(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getFeatures(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd: (Do not) filter features
getFeatures(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: (Do not) filter features
getFeatures() - Method in class com.github.seqware.queryengine.model.FeatureSet: Get the list of features associated with this feature set.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.FeatureList: Returns a list of features at this location, should not be modified.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Get the list of features associated with this feature set.
getFeatures() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Get the list of features associated with this feature set.
getFeatures(int, FeatureSet) - Method in interface com.github.seqware.queryengine.model.QueryInterface: (Do not) filter features
getFeatures(String, Integer, Integer, Integer, Integer, Integer, Integer, Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getFeatures.
getFeatures() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getFeatures.
getFeatures(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getFeatures.
getFeatures() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getFeatures.
getFeatures(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getFeatures.
getFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getFeaturesBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getFeaturesBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getFeaturesBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd: Filter features by a range of attributes.
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Filter features by a range of attributes.
getFeaturesByAttributes(int, FeatureSet, RPNStack) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Filter features by a range of attributes.
getFeaturesByPlugin(int, Class<? extends AnalysisPluginInterface>, FeatureSet, Object...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Call an arbitrary installed plug-in by class and initiate it
getFeaturesByPlugin(int, Class<? extends AnalysisPluginInterface>, FeatureSet, Object...) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Call an arbitrary installed plug-in by class and initiate it
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd: filter features that overlap with a given range
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: filter features that overlap with a given range
getFeaturesByRange(int, FeatureSet, QueryInterface.Location, String, long, long) - Method in interface com.github.seqware.queryengine.model.QueryInterface: filter features that overlap with a given range
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd: filter features with tags.
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: filter features with tags.
getFeaturesByTag(int, FeatureSet, String, String, String) - Method in interface com.github.seqware.queryengine.model.QueryInterface: filter features with tags.
getFeaturesByTag(String, Integer, Integer, Integer, Integer, Integer, Integer, Integer, Integer, String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getFeaturesByTag.
getFeaturesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getFeaturesByTag.
getFeaturesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getFeaturesByTag.
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getFeaturesCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getFeaturesCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getFeaturesCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getFeatureSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
getFeatureSetBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getFeatureSetCount(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd: Get the number of features in a feature set
getFeatureSetCount(int, FeatureSet) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Get the number of features in a feature set
getFeatureSetCount(int, FeatureSet) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Get the number of features in a feature set
getFeatureSetID() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field featureSetID.
getFeatureSetID() - Method in class com.github.seqware.queryengine.util.FSGID: Get the ID for the associated feature set
getFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getFeatureSetIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getFeatureSetIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getFeatureSetIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getFeatureSetIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getFeatureSetIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getFeatureSetIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getFeatureSetIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getFeatureSetIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getFeatureSetIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getFeatureSetIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getFeatureSetIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getFeatureSetIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getFeatureSetIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getFeatureSetIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getFeatureSetIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getFeatureSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getFeatureSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getFeatureSetOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
getFeatureSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: getFeatureSets.
getFeatureSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getFeatureSets.
getFeatureSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getFeatureSets.
getFeatureSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getFeatureSets.
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getFeaturesList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getFeaturesList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getFeaturesList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getFeaturesOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getFeaturesOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getFeaturesOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getFeaturesOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getFeaturesOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getFeaturesOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getFeaturesTags.
getFeaturesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getFeaturesTags.
getFeaturesTags() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getFeaturesTags.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getFeaturesUnordered.
getFeaturesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getFeaturesUnordered.
getFeaturesUnordered() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getFeaturesUnordered.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getFeatureTagsBySearch.
getFeatureTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getFeatureTagsBySearch.
getFile() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field file.
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getFile.
getFile(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getFile.
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getFile.
getFile(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getFile.
getFile() - Method in class net.sourceforge.seqware.common.model.FileAttribute: Getter for the field file.
getFile() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field file.
getFile() - Method in class net.sourceforge.seqware.common.model.ShareFile: Getter for the field file.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES: Gets the value of the file property.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES: Gets the value of the file property.
getFILE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES: Gets the value of the file property.
getFile() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Getter for the field file.
getFileAttributeId() - Method in class net.sourceforge.seqware.common.model.FileAttribute: Getter for the field fileAttributeId.
getFileAttributes(Integer) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService: Returns a complete set of attributes for a give File.
getFileAttributes(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl: Returns a complete set of attributes for a give File.
getFileAttributes() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field fileAttributes.
getFileAttributes() - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributesResource: getFileAttributes.
getFileAttributes() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributesServerResource: getFileAttributes.
getFileAttributeService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field fileAttributeService.
getFileAttributeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getFileAttributeServiceBean.
getFileHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: getFileHtml.
getFileHtml(Processing, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil: getFileHtml.
getFileHtml(Processing, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil: getFileHtml.
getFileId() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field fileId.
getFileMetaType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field fileMetaType.
getFileMetaType() - Method in class net.sourceforge.solexatools.util.SummaryLine: Getter for the field fileMetaType.
getFilename() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getFileName() - Method in class net.sourceforge.seqware.common.model.File: getFileName.
getFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Gets the file name.
getFilename() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE: Gets the value of the filename property.
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE: Gets the value of the filename property.
getFilename() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE: Gets the value of the filename property.
getFileName(String) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController: getFileName.
getFileOne() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field fileOne.
getFilePath() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field filePath.
getFilePath() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getFilePath() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field filePath.
getFilePath(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getFilePath.
getFilePath() - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Getter for the field filePath.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.FileService: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.FileService: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: getFiles.
getFiles(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: getFiles.
getFiles(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: getFiles.
getFiles(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: getFiles.
getFiles(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: getFiles.
getFiles() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field files.
getFiles() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field files.
getFiles() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field files.
getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
getFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the files property.
getFILES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the files property.
getFiles(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.BulkUtil: getFiles.
getFiles() - Method in class net.sourceforge.solexatools.util.SummaryLine: Getter for the field files.
getFiles_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field files_url.
getFilesArray() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: Getter for the field filesArray.
getFileService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field fileService.
getFileService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Getter for the field fileService.
getFileServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getFileServiceBean.
getFileSize(String) - Static method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: getFileSize.
getFilesNumber() - Method in class net.sourceforge.solexatools.util.FileFinder: Getter for the field filesNumber.
getFileStatus() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getFileSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getFileTwo() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field fileTwo.
getFileTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field fileTwoURL.
getFileType() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field fileType.
getFileType() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field fileType.
getFileType() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field fileType.
getFiletype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE: Gets the value of the filetype property.
getFiletype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE: Gets the value of the filetype property.
getFileTypeId() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field fileTypeId.
getFileTypeId() - Method in class net.sourceforge.seqware.common.model.FileType: Getter for the field fileTypeId.
getFileTypeId() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field fileTypeId.
getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator: Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Getter for the field fileTypeService.
getFileTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController: Getter for the field fileTypeService.
getFileUploadService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field fileUploadService.
getFileURL() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field fileURL.
getFileURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field fileURL.
getFileValidationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getFileValidationServiceBean.
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin: getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin: getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin: getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin: getFilter.
getFilter() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin: getFilter.
getFinalResult() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: Blocking call to get the final result of the plug-in
getFinalResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Blocking call to get the final result of the plug-in
getFinalResult() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin: Blocking call to get the final result of the plug-in
getFinalResult() - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin: Blocking call to get the final result of the plug-in
getFinishedCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: getFinishedCount.
getFinishedCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: getFinishedCount.
getFinishedTimestamp() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field finishedTimestamp.
getFirstId(String) - Static method in class net.sourceforge.solexatools.util.Constant: getFirstId.
getFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getFirstName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getFirstName() - Method in class com.github.seqware.queryengine.model.User: Get first name
getFirstName() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field firstName.
getFirstName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Getter for the field firstName.
getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field flowCount.
getFlowCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field flowCount.
getFLOWCOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS: Gets the value of the flowcount property.
getFLOWCOUNT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454: Gets the value of the flowcount property.
getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field flowSequence.
getFlowSequence() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field flowSequence.
getFLOWSEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS: Gets the value of the flowsequence property.
getFLOWSEQUENCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454: Gets the value of the flowsequence property.
getFolderStore() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field folderStore.
getFolderStore() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field folderStore.
getForceRunAll() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getFormatCode() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the formatCode property.
getFrame() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field frame.
getFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
getFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getFriendlyRowkey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
getFriendlyRowKey() - Method in class com.github.seqware.queryengine.util.SGID: Getter for the field friendlyRowKey.
getFullName() - Method in class net.sourceforge.seqware.common.model.Workflow: getFullName.
getFuzzyStartPositionMax() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field fuzzyStartPositionMax.
getFuzzyStopPositionMin() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field fuzzyStopPositionMin.
getGcrOutputFile() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
getGeneChr() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field geneChr.
getGeneId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field geneId.
getGeneId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field geneId.
getGenomeId() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field genomeId.
getGenomicSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field genomicSequence.
getGrammarFileName() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: getGrammarFileName.
getGrammarFileName() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: getGrammarFileName.
getGroup() - Method in class com.github.seqware.queryengine.model.interfaces.ACL: Get the group for the object
getGroup() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field group.
getGroups() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: Get all groups
getGroups() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Get all groups
getGroups() - Method in interface com.github.seqware.queryengine.model.QueryInterface: Get all groups
getGroups() - Method in class com.github.seqware.queryengine.model.User: Get list of groups that this user is a part of
getGroups() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getGroups.
getGroupSGID() - Method in class com.github.seqware.queryengine.model.interfaces.ACL: Get the group for the object
getGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getGrp() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
getGrpBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getGrpOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getGrpOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getGrpOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
getGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getGrps(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getGrpsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getGrpsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getGrpsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getGrpsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getGrpsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getGrpsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getGrpsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getGrpsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getGrpsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getGrpsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getGrpsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getGrpsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getGrpsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getGrpsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getHandle() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the handle property.
getHBaseClass() - Method in class com.github.seqware.queryengine.model.Feature: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.FeatureList: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.Tag: Get the model class for the HBase where this obj should be stored
getHBaseClass() - Method in class com.github.seqware.queryengine.model.User: Get the model class for the HBase where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.Feature: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.FeatureList: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.Tag: Get the HBase table prefix where this obj should be stored
getHBasePrefix() - Method in class com.github.seqware.queryengine.model.User: Get the HBase table prefix where this obj should be stored
getHeader() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getHeader() - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource: getHeader.
getHELICOS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Gets the value of the helicos property.
getHOLD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Gets the value of the hold property.
getHoldForPeriod() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Gets the value of the holdForPeriod property.
getHoldUntilDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Gets the value of the holdUntilDate property.
getHost() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field host.
getHost() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field host.
getHost() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field host.
getHtml() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field html.
getHtml() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field html.
getHtml() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field html.
getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: getHtml.
getHtml(Object, Registration, List<String>, String) - Static method in class net.sourceforge.solexatools.util.StudyHtmlUtil: getHtml.
getHtml(Object, Registration, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getHtml.
getHtml(WorkflowRun, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil: getHtml.
getHtml(Sample, WorkflowRun, Registration, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil: getHtml.
getHtml(Processing, WorkflowRun, Registration, String, List<String>, String) - Static method in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil: getHtml.
getHttpInputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: getHttpInputStream.
getHYBRIDASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the hybridassembly property.
getId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getId() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getId() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.IUSLink: Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.LaneLink: Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.SampleLink: Getter for the field id.
getId() - Method in class net.sourceforge.seqware.common.model.StudyLink: Getter for the field id.
getId() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob: get the job id
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field id.
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model: Getter for the field id.
getId() - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface: getId.
getId() - Method in class net.sourceforge.seqware.queryengine.backend.model.StringId: Getter for the field id.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK: Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK: Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK: Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK: Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK: Gets the value of the id property.
getID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK: Gets the value of the id property.
getId() - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource: Getter for the field id.
getId(String) - Static method in class net.sourceforge.solexatools.util.Constant: getId.
getIdentitySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field identitySamples.
getIdsSelectedLane(HttpServletRequest, WorkflowParam) - Method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getIdsSelectedLane.
getILLUMINA() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Gets the value of the illumina property.
getIndividualName() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field individualName.
getInfo() - Method in class net.sourceforge.seqware.common.model.FileType: getInfo.
getInfo() - Method in class net.sourceforge.solexatools.util.PageInfo: Getter for the field info.
getInformOnError() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT: Gets the value of the informOnError property.
getInformOnStatus() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT: Gets the value of the informOnStatus property.
getIniFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field iniFile.
getInput() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field input.
getInput() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field input.
getInputAlgorithm() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field inputAlgorithm.
getInputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field inputFiles.
getInstance() - Static method in class net.sourceforge.seqware.common.ContextImpl: getInstance.
getInstitution() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field institution.
getInstitution() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Getter for the field institution.
getInstrumentModel() - Method in class net.sourceforge.seqware.common.model.Platform: Getter for the field instrumentModel.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS: Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA: Gets the value of the instrumentmodel property.
getINSTRUMENTMODEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454: Gets the value of the instrumentmodel property.
getInstrumentModel() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the instrumentModel property.
getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field instrumentName.
getInstrumentName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field instrumentName.
getInstrumentName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the instrumentName property.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Internal parameters that can be used to pass information to the Mapper and Reducers.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesAllPlugin: Internal parameters that can be used to pass information to the Mapper and Reducers.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByAttributesPlugin: Internal parameters that can be used to pass information to the Mapper and Reducers.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByRangePlugin: Internal parameters that can be used to pass information to the Mapper and Reducers.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByTagsPlugin: Internal parameters that can be used to pass information to the Mapper and Reducers.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin: Internal parameters that can be used to pass information to the Mapper and Reducers.
getInternalParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin: Internal parameters that can be used to pass information to the Mapper and Reducers.
getInvitationCode() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field invitationCode.
getInvoice() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field invoice.
getInvoiceId() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field invoiceId.
getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController: Getter for the field invoiceService.
getInvoiceService() - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController: Getter for the field invoiceService.
getIsEnd() - Method in class net.sourceforge.solexatools.util.PageInfo: Getter for the field isEnd.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field isHasFile.
getIsHasFile() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field isHasFile.
getIsInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams: Getter for the field isInvitationCode.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field isSelected.
getIsSelected() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field isSelected.
getIsStart() - Method in class net.sourceforge.solexatools.util.PageInfo: Getter for the field isStart.
getItemRgb() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field itemRgb.
getIus() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.IUSAttribute: Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.IUSLink: Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field ius.
getIUS() - Method in class net.sourceforge.seqware.common.model.Lane: getIUS.
getIUS() - Method in class net.sourceforge.seqware.common.model.Processing: getIUS.
getIus() - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Getter for the field ius.
getIUS() - Method in class net.sourceforge.seqware.common.model.Sample: getIUS.
getIus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Getter for the field ius.
getIus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field ius.
getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem: Getter for the field ius.
getIus() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Getter for the field ius.
getIusAttributeId() - Method in class net.sourceforge.seqware.common.model.IUSAttribute: Getter for the field iusAttributeId.
getIusAttributes() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field iusAttributes.
getIusFiles() - Method in interface net.sourceforge.seqware.webservice.resources.tables.IusFilesResource: List files associated with Ius.
getIusFiles() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource: List files associated with Ius.
getIUSHtml(IUS, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getIUSHtml.
getIusId() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field iusId.
getIusLinkId() - Method in class net.sourceforge.seqware.common.model.IUSLink: Getter for the field iusLinkId.
getIusLinks() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field iusLinks.
getIusService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field iusService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController: Getter for the field iusService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: getIUSService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: getIUSService.
getIusService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field iusService.
getIUSService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: getIUSService.
getIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getIUSServiceBean.
getIusSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getIusSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getIusTag() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getJobObject() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
getJobs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow: get all jobs in current workflow
getJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field joinDevelopersMailingList.
getJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field joinUsersMailingList.
getJsonEscapeAlgorithm() - Method in class net.sourceforge.seqware.common.model.Processing: getJsonEscapeAlgorithm.
getJsonEscapeDefaultValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: getJsonEscapeDefaultValue.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Experiment: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.File: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.IUS: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Lane: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Processing: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Sample: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.SequencerRun: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Study: getJsonEscapeDescription.
getJsonEscapeDescription() - Method in class net.sourceforge.seqware.common.model.Workflow: getJsonEscapeDescription.
getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Experiment: getJsonEscapeDescription200.
getJsonEscapeDescription200() - Method in class net.sourceforge.seqware.common.model.Study: getJsonEscapeDescription200.
getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: getJsonEscapeDisplayName.
getJsonEscapeDisplayName() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: getJsonEscapeDisplayName.
getJsonEscapeFileName() - Method in class net.sourceforge.seqware.common.model.File: getJsonEscapeFileName.
getJsonEscapeFullName() - Method in class net.sourceforge.seqware.common.model.Workflow: getJsonEscapeFullName.
getJsonEscapeKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: getJsonEscapeKey.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Experiment: getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.IUS: getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Lane: getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Sample: getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.SequencerRun: getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.Workflow: getJsonEscapeName.
getJsonEscapeName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: getJsonEscapeName.
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Experiment: getJsonEscapeTitle.
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Sample: getJsonEscapeTitle.
getJsonEscapeTitle() - Method in class net.sourceforge.seqware.common.model.Study: getJsonEscapeTitle.
getJsonEscapeType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: getJsonEscapeType.
getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: getJsonEscapeValue.
getJsonEscapeValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: getJsonEscapeValue.
getKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getKey() - Method in class com.github.seqware.queryengine.model.Tag: Get the key.
getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field key.
getKey() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Getter for the field key.
getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument: Getter for the field key.
getKey() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile: Getter for the field key.
getKeyIndex() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field keyIndex.
getKeyValueFromFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: getKeyValueFromFile.
getKeyvalues() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model: Getter for the field keyvalues.
getLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.IUSLink: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.LaneLink: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.SampleLink: Getter for the field label.
getLabel() - Method in class net.sourceforge.seqware.common.model.StudyLink: Getter for the field label.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK: Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK: Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK: Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK: Gets the value of the label property.
getLABEL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK: Gets the value of the label property.
getLabName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the labName property.
getLane() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.LaneLink: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.common.model.ShareLane: Getter for the field lane.
getLane() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getLane() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem: Getter for the field lane.
getLane1() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane1.
getLane2() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane2.
getLane3() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane3.
getLane4() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane4.
getLane5() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane5.
getLane6() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane6.
getLane7() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane7.
getLane8() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lane8.
getLane_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field lane_url.
getLaneAttributeId() - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Getter for the field laneAttributeId.
getLaneAttributes() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field laneAttributes.
getLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO: Getter for the field laneCount.
getLaneHtml(Lane, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getLaneHtml.
getLaneHtml(Lane, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getLaneHtml.
getLaneId() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field laneId.
getLaneIndex() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field laneIndex.
getLaneLinkId() - Method in class net.sourceforge.seqware.common.model.LaneLink: Getter for the field laneLinkId.
getLaneLinks() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field laneLinks.
getLaneName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getLanes() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field lanes.
getLanes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field lanes.
getLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.validation.LaneValidator: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field laneService.
getLaneService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Getter for the field laneService.
getLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getLaneServiceBean.
getLaneSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getLaneSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getLastName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getLastName() - Method in class com.github.seqware.queryengine.model.User: Get last name
getLastName() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field lastName.
getLastName() - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Getter for the field lastName.
getLatestAtomByRowKey(String, Class<T>) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Find an atom in the back-end when a specific class is known and a specific row key is known
getLatestAtomByRowKey(String, Class<T>) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Find an atom in the back-end when a specific class is known and a specific row key is known
getLatestAtomBySGID(SGID) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Find the latest object in the back-end by a globally unique SGID while ignoring the timestamp
getLatestAtomBySGID(SGID, Class<T>) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Find an object in the back-end when a specific class is known while ignoring the timestamp
getLatestAtomBySGID(SGID) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Deprecated. It is much more efficient to retrieve an Atom when you know the class
getLatestAtomBySGID(SGID, Class<T>) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Find an object in the back-end when a specific class is known while ignoring the timestamp
getLatestModel(String, TupleBinding, HTable, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: This is actually a pretty dangerous method since just the most recent biallelic variant will be returned.
getLayout() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field layout.
getLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
getLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getLeastSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
getLength() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field length.
getLibraries() - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl: Returns a complete list of libraries.
getLibraries(Map<String, String>) - Method in class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl: Returns a list of libraries that match all attributes provided in the give attributes Map.
getLibraries() - Method in interface net.sourceforge.seqware.common.business.LibraryService: Returns a complete list of libraries.
getLibraries(Map<String, String>) - Method in interface net.sourceforge.seqware.common.business.LibraryService: Returns a list of libraries that match all attributes provided in the give attributes Map.
getLibraries(String, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate: Returns list of libraries that contain the attribute attributeName=attributeValue.
getLibraries() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate: Returns a complete list of libraries.
getLibraries(String, String) - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO: Returns list of libraries that contain the attribute attributeName=attributeValue.
getLibraries() - Method in interface net.sourceforge.seqware.common.dao.LibraryDAO: Returns a complete list of libraries.
getLibraries() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource: getLibraries.
getLIBRARYCONSTRUCTIONPROTOCOL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Gets the value of the libraryconstructionprotocol property.
getLIBRARYDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Gets the value of the librarydescriptor property.
getLibraryId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto: Getter for the field libraryId.
getLIBRARYLAYOUT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Gets the value of the librarylayout property.
getLIBRARYNAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Gets the value of the libraryname property.
getLibrarySamples() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field librarySamples.
getLibrarySelection() - Method in class net.sourceforge.seqware.common.model.Lane
getLIBRARYSELECTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Gets the value of the libraryselection property.
getLibrarySelectionId() - Method in class net.sourceforge.seqware.common.model.LibrarySelection: Getter for the field librarySelectionId.
getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getLibrarySelections() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getLibrarySelections.
getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getLibrarySelections() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getLibrarySelectionService() - Method in class net.sourceforge.seqware.common.ContextImpl
getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field librarySelectionService.
getLibrarySelectionService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Getter for the field librarySelectionService.
getLibrarySelectionServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getLibrarySelectionServiceBean.
getLibraryService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field libraryService.
getLibraryServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getLibraryServiceBean.
getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getLibrarySource() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getLibrarySource.
getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getLibrarySource() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getLibrarySource() - Method in class net.sourceforge.seqware.common.model.Lane
getLIBRARYSOURCE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Gets the value of the librarysource property.
getLibrarySourceId() - Method in class net.sourceforge.seqware.common.model.LibrarySource: Getter for the field librarySourceId.
getLibrarySourceService() - Method in class net.sourceforge.seqware.common.ContextImpl
getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field librarySourceService.
getLibrarySourceService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Getter for the field librarySourceService.
getLibrarySourceServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getLibrarySourceServiceBean.
getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getLibraryStrategies() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getLibraryStrategies.
getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getLibraryStrategies() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getLibraryStrategy() - Method in class net.sourceforge.seqware.common.model.Lane
getLIBRARYSTRATEGY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Gets the value of the librarystrategy property.
getLibraryStrategyId() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy: Getter for the field libraryStrategyId.
getLibraryStrategyService() - Method in class net.sourceforge.seqware.common.ContextImpl
getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field libraryStrategyService.
getLibraryStrategyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Getter for the field libraryStrategyService.
getLibraryStrategyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getLibraryStrategyServiceBean.
getLibraryType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Getter for the field libraryType.
getList() - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.FileList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.IUSList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LaneList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.OrganismList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.PlatformList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.SampleList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList: getList.
getList() - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2: getList.
getLocatableModels(SecondaryDatabase, TupleBinding, String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getLocatableModels.
getLocatableModels(String, String, TupleBinding, String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getLocatableModels.
getLock() - Method in class com.github.seqware.queryengine.system.importers.Importer: getLock.
getLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock: Deprecated. Lock file, do not clear on exit
getLock(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock: Deprecated. Lock file, but give option to free lock when the JVM exits.
getLock(int, int) - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock: Deprecated. getLock.
getLock() - Method in class net.sourceforge.seqware.queryengine.tools.importers.Importer: getLock.
getLongName() - Method in class net.sourceforge.seqware.common.model.Platform: getLongName.
getLS454() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Gets the value of the ls454 property.
getMainClass() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: return the main class for a Java job, or the script.pl for a perl Job
getManager() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get the model manager for this Atom
getMap() - Method in class com.github.seqware.queryengine.util.obo.OboFileHandlerHack: Getter for the field map.
getMaxCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field maxCoverage.
getMaxCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field maxCoverage.
getMaxCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field maxCoverage.
getMaximumMappingQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field maximumMappingQuality.
getMaxLockers() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field maxLockers.
getMaxLockObjects() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field maxLockObjects.
getMaxLocks() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field maxLocks.
getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
getMaxMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
getMaxMemory() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
getMD5Hash(String) - Method in class net.sourceforge.seqware.common.metadata.Metadata: getMD5Hash.
getMd5sum() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field md5sum.
getMd5sum() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getMd5sum() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getMd5sum() - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Getter for the field md5sum.
getMeaning() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
getMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF: Gets the value of the member property.
getMEMBER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS: Gets the value of the member property.
getMEMBERS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Gets the value of the members property.
getMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getMemReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field memReq.
getMetadata() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: Getter for the field metadata.
getMetadata() - Method in class net.sourceforge.seqware.pipeline.module.Module: Getter for the field metadata.
getMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getMetadata.
getMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getMetadata.
getMetadata_output_dir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getMetadata_output_file_prefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getMetadataOutputPrefix() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
getMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getMetaType() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field metaType.
getMetaType() - Method in class net.sourceforge.seqware.common.model.FileType: Getter for the field metaType.
getMetaType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getMetaType() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getMetaType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Getter for the field metaType.
getMimeType() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getMinCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field minCoverage.
getMinCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field minCoverage.
getMinCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field minCoverage.
getMinObservations() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field minObservations.
getMinObservationsPerStrand() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field minObservationsPerStrand.
getMinPercent() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field minPercent.
getMinSnpQuality() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field minSnpQuality.
getMinSnpQuality() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field minSnpQuality.
getMinSNVPhred() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field minSNVPhred.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getMismatch.
getMismatch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatch.
getMismatch(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getMismatch.
getMismatchAAChangeBlosumScore() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchAAChangeBlosumScore.
getMismatchAminoAcidChange() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchAminoAcidChange.
getMismatchChr() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchChr.
getMismatchCodonChange() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchCodonChange.
getMismatchCodonPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchCodonPosition.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatches.
getMismatches(String, int, int) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatches.
getMismatches(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatches.
getMismatches() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getMismatches.
getMismatches(String, int, int) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getMismatches.
getMismatches(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getMismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication: Getter for the field mismatches.
getMismatches() - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion: Getter for the field mismatches.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getMismatchesByTag.
getMismatchesByTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatchesByTag.
getMismatchesByTag(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getMismatchesByTag.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatchesTags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: Get access to an iterator containing all the mismatch tags.
getMismatchesTags() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatchesTags.
getMismatchesTags() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getMismatchesTags.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getMismatchesUnordered.
getMismatchesUnordered() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatchesUnordered.
getMismatchesUnordered() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getMismatchesUnordered.
getMismatchId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchId.
getMismatchStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchStart.
getMismatchStop() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchStop.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getMismatchTagsBySearch.
getMismatchTagsBySearch(String) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: getMismatchTagsBySearch.
getMismatchType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mismatchType.
getModel(String, TupleBinding, HTable, String, String, Long) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getModel.
getModel(String, String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getModel.
getModelAndView(String, ModelAndView) - Static method in class net.sourceforge.solexatools.util.StudyBuildTree: getModelAndView.
getModelManager() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory: Return a new model manager to create and keep track of entities
getModels(SecondaryDatabase, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getModels.
getModels(HTable, Filter, TupleBinding, String, String, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getModels.
getModels(HTable, Scan, Filter, TupleBinding, String, String, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getModels.
getModels(String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getModels.
getModelsByTag(SecondaryDatabase, TupleBinding, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getModelsByTag.
getModelsByTag(String, HTable, HTable, TupleBinding, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: getModelsByTag.
getModelsByTag(String, String, String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getModelsByTag.
getModelsTags(SecondaryDatabase, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: Get access to an iterator containing all the mismatch tags.
getModelsTags(String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getModelsTags.
getModelsTags(String, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getModelsTags.
getModelsUnordered(Database, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: getModelsUnordered.
getModelsUnordered(String, String, TupleBinding) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: getModelsUnordered.
getModelTags(HTable) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: Other methods expect this to return a SeqWareIterator and not a HashMap.
getMODIFY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Gets the value of the modify property.
getModuleType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule: Getter for the field moduleType.
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getMolBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getMolOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getMolOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
getMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getMostSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
getMULTIPLIER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Gets the value of the multiplier property.
getMutatedGenomicSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mutatedGenomicSequence.
getMutatedTranslatedSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field mutatedTranslatedSequence.
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
getName() - Method in interface com.github.seqware.queryengine.model.AnalysisSet: Get the name of the analysisSet
getName() - Method in interface com.github.seqware.queryengine.model.Group: Get the name of the group
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet: Get the name of the analysisSet
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup: Get the name of the group
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference: The name of this reference (ex: "hg 19")
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet: Get the name of the reference set
getName() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: Get the name of the tag set
getName() - Method in interface com.github.seqware.queryengine.model.Reference: The name of this reference (ex: "hg 19")
getName() - Method in interface com.github.seqware.queryengine.model.ReferenceSet: Get the name of the reference set
getName() - Method in interface com.github.seqware.queryengine.model.TagSet: Get the name of the tag set
getName() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.LibrarySelection: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.LibrarySource: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Organism: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Platform: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.StudyType: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
getName() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule: getName.
getName() - Method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module: getName.
getName() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the name property.
getName() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT: Gets the value of the name property.
getName() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field name.
getName() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto: Getter for the field name.
getName() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
getNameNode() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field nameNode.
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile: getNamespace.
getNamespace() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
getNcbiTaxId() - Method in class net.sourceforge.seqware.common.model.Organism: Getter for the field ncbiTaxId.
getNcbiTaxonomyId() - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto: Getter for the field ncbiTaxonomyId.
getNestedTags(TagSet) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Convenience method for getNestedTags(String tagSet)
getNestedTags(String) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get tags that have been sorted into a structure of Nested Maps.
getNestedTags(String) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable: Get tags that have been sorted into a structure of Nested Maps.
getNestedTags(TagSet) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable: Convenience method for getNestedTags(String tagSet)
getNetwork() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getNetworkReq() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field networkReq.
getNewStudyType() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE: Gets the value of the newStudyType property.
getNewType() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field newType.
getNodeHtml(Processing, Registration, String, boolean, boolean, boolean, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getNodeHtml.
getNodeHtml(Processing, Registration) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getNodeHtml.
getNodeIds(Object) - Static method in class net.sourceforge.solexatools.util.FindChildUtil: getNodeIds.
getNominalLength() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field nominalLength.
getNOMINALLENGTH() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED: Gets the value of the nominallength property.
getNominalSdev() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field nominalSdev.
getNOMINALSDEV() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED: Gets the value of the nominalsdev property.
getNotes() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field notes.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD: Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY: Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE: Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS: Gets the value of the notes property.
getNotes() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE: Gets the value of the notes property.
getNotRunned() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field notRunned.
getNumber() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
getNumberChannels() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the numberChannels property.
getNUMBEROFLEVELS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Gets the value of the numberoflevels property.
getNUMBEROFREADSPERSPOT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC: Gets the value of the numberofreadsperspot property.
getNumQueries() - Method in interface com.github.seqware.queryengine.system.exporters.QueryDumperInterface: Return the number of queries that we wish to run consecutively
getOffspringProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field offspringProcessings.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.module.Module: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.basicQC: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.dqc: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: getOptionParser is an internal method to parse command line args.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.Compress: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: getOptionParser.
getOptionParser() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: getOptionParser.
getOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getOrganism() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getOrganism() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet: Get the organism associated with this reference set
getOrganism() - Method in interface com.github.seqware.queryengine.model.ReferenceSet: Get the organism associated with this reference set
getOrganism() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field organism.
getOrganism() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field organism.
getOrganism() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field organism.
getOrganismId() - Method in class net.sourceforge.seqware.common.model.Organism: Getter for the field organismId.
getOrganismId() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field organismId.
getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getOrganisms() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getOrganisms.
getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getOrganisms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getOrganismService() - Method in class net.sourceforge.seqware.common.ContextImpl
getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Getter for the field organismService.
getOrganismService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Getter for the field organismService.
getOrganismServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getOrganismServiceBean.
getORIENTATION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED: Gets the value of the orientation property.
getOriginalFileName() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Getter for the field originalFileName.
getOs() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
getOutput() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread: Getter for the field output.
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: Getter for the field outputDir.
getOutputDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
getOutputFilename() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Getter for the field outputFilename.
getOutputFilename() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field outputFilename.
getOutputFiles() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field outputFiles.
getOwner() - Method in class com.github.seqware.queryengine.model.interfaces.ACL: Get the owner for the object
getOwner() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field owner.
getOwner() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field owner.
getOwnerId() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field ownerId.
getOwnerSGID() - Method in class com.github.seqware.queryengine.model.interfaces.ACL: Get the owner for the object
getPage() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Getter for the field page.
getPageInfo(HttpServletRequest, String, List, List, String, String, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil: getPageInfo.
getPageInfoSD(HttpServletRequest, String, List, List, MessageSourceAccessor) - Static method in class net.sourceforge.solexatools.util.PaginationUtil: getPageInfoSD.
getPageNumber(HttpServletRequest, Study, List<Study>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil: getPageNumber.
getPaidAmount() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field paidAmount.
getPAIRED() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT: Gets the value of the paired property.
getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field pairedEnd.
getPairedEnd() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field pairedEnd.
getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field pairedFilePath.
getPairedFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field pairedFilePath.
getPairedOrientation() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field pairedOrientation.
getParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getParameters() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
getParameters() - Method in class com.github.seqware.queryengine.kernel.RPNStack: Returns the parameters of the argument stack, i.e., everything that is not a constant and considered to be a variable.
getParameters() - Method in class com.github.seqware.queryengine.model.Analysis: Get the parameters for this particular creation of an analysis plug-in
getParameters() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field parameters.
getParameters() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field parameters.
getParameters() - Method in class net.sourceforge.seqware.pipeline.module.Module: Getter for the field parameters.
getParams() - Method in class net.sourceforge.solexatools.util.SummaryLine: Getter for the field params.
getPARENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the parent property.
getParent_accessions() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getParentAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
getParentLane(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: getParentLane.
getParentProcessing(Processing, Integer) - Static method in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: getParentProcessing.
getParentProcessingAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Getter for the field parentProcessingAccession.
getParentProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field parentProcessings.
getParents() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field parents.
getParents() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field parents.
getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
getParents() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: add all parent jobs
getParents() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
getParentUrls() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field parentUrls.
getParentWorkflowAccessions() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getPassword() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getPassword() - Method in class com.github.seqware.queryengine.model.User: A hashed password for the user
getPassword() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field password.
getPassword() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field password.
getPasswordHint() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field passwordHint.
getPathToFirstFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field pathToFirstFile.
getPathToSecondFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field pathToSecondFile.
getPeakMemory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getPeakThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getPegasusConfigDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getPending() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field pending.
getPermanentBundleLocation() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field permanentBundleLocation.
getPermBundleLocation() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field permBundleLocation.
getPermissions() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Get permissions for the subject.
getPermissions() - Method in interface com.github.seqware.queryengine.model.interfaces.ACLable: Get permissions for the subject.
getPfn() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
getPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getPhase() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getPhase() - Method in class com.github.seqware.queryengine.model.Feature: (GVF: The phase column is not used in GVF, but is maintained with the placeholder '.' (period) for compatibility with GFF3 and tools that conform to the GFF3 specification (and do change it))
getPipelineJarPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
getPlatform() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field platform.
getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field platform.
getPlatform() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field platform.
getPLATFORM() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the platform property.
getPlatformId() - Method in class net.sourceforge.seqware.common.model.Platform: Getter for the field platformId.
getPlatformInt() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field platformInt.
getPlatformInt() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field platformInt.
getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getPlatforms() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getPlatforms.
getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getPlatforms() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getPlatformService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Getter for the field platformService.
getPlatformService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController: Getter for the field platformService.
getPlatformServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getPlatformServiceBean.
getPlugin() - Method in class com.github.seqware.queryengine.model.Analysis: Get analysis plugin
getPlugin() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Get analysis plugin
getPmi() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field pmi.
getPmi() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field pmi.
getPostgresqlPersistenceStrategy() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field postgresqlPersistenceStrategy.
getPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getPragma() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getPragma() - Method in class com.github.seqware.queryengine.model.Feature: GVF provides pragmas that are file-wide.
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getPrecedingIDBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getPrecedingIDBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getPrecedingIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getPrecedingIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getPrecedingIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getPrecedingSGID() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Used in back-end to get previous version ID
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getPrecedingVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Returns the subject (if any) that represents a previous version.
getPrecedingVersion() - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable: Returns the subject (if any) that represents a previous version.
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getPrecedingVersionBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
getPrecedingVersionOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getPrecedingVersionOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
getPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getPredicate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getPredicate() - Method in class com.github.seqware.queryengine.model.Tag: Get the predicate.
getPricePerUnit() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field pricePerUnit.
getPricePerUnitString() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field pricePerUnit.
getPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow: getPrivate.
getProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field process.
getProcessedCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: getProcessedCnt.
getProcessedCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: getProcessedCnt.
getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.Lane: getProcessedCnt.
getProcessedCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun: getProcessedCnt.
getProcessedCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field processedCount.
getProcessExitStatus() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field processExitStatus.
getProcessExitStatus() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field processExitStatus.
getProcessing() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Getter for the field processing.
getProcessing() - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Getter for the field processing.
getPROCESSING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the processing property.
getProcessingAccession() - Method in class net.sourceforge.seqware.pipeline.module.Module: Getter for the field processingAccession.
getProcessingAttributeId() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: Getter for the field processingAttributeId.
getProcessingAttributes() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field processingAttributes.
getProcessingByChildId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Getter for the field processingByChildId.
getProcessingByParentId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Getter for the field processingByParentId.
getProcessingCnt(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: getProcessingCnt.
getProcessingCnt(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: getProcessingCnt.
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.Lane: getProcessingCnt.
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRun: getProcessingCnt.
getProcessingCnt() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: getProcessingCnt.
getProcessingCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field processingCount.
getProcessingExperimentServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingExperimentServiceBean.
getProcessingExperimentsId() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Getter for the field processingExperimentsId.
getProcessingExperimentsService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingExperimentsService.
getProcessingHtml(Processing, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getProcessingHtml.
getProcessingId() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field processingId.
getProcessingIusId() - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Getter for the field processingIusId.
getProcessingIusService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingIusService.
getProcessingIUSServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingIUSServiceBean.
getProcessingLaneService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingLaneService.
getProcessingLaneServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingLaneServiceBean.
getProcessingLanesId() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Getter for the field processingLanesId.
getProcessingRelationshipId() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Getter for the field processingRelationshipId.
getProcessingRelationshipService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingRelationshipService.
getProcessingRelationshipServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingRelationshipServiceBean.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field processings.
getProcessings() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field processings.
getProcessingSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingSampleServiceBean.
getProcessingSamplesId() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Getter for the field processingSamplesId.
getProcessingSamplesService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingSamplesService.
getProcessingsByWorkflow(WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems: getProcessingsByWorkflow.
getProcessingSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingSequencerRunService.
getProcessingSequencerRunsId() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Getter for the field processingSequencerRunsId.
getProcessingSequencerRunsServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingSequencerRunsServiceBean.
getProcessingService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field processingService.
getProcessingService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Getter for the field processingService.
getProcessingServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingServiceBean.
getProcessingStudiesId() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Getter for the field processingStudiesId.
getProcessingStudiesService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field processingStudiesService.
getProcessingStudiesServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getProcessingStudiesServiceBean.
getProcStatuses(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: getProcStatuses.
getProcStatuses(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: getProcStatuses.
getProjectId() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field projectId.
getProjectId() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field projectId.
getPROJECTID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Gets the value of the projectid property.
getProperty(String) - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools: getProperty.
getProperty(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.util.EnvUtil: getProperty.
getPROTECT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Gets the value of the protect property.
getProvisionedPath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
getPublic() - Method in class net.sourceforge.seqware.common.model.Workflow: getPublic.
getQCREPORT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the qcreport property.
getQtype() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Gets the value of the qtype property.
getQualityMultiplier() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field qualityMultiplier.
getQualityNumberOfLevels() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field qualityNumberOfLevels.
getQualityScorer() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field qualityScorer.
getQUALITYSCORER() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Gets the value of the qualityscorer property.
getQUALITYSCORES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING: Gets the value of the qualityscores property.
getQualityType() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field qualityType.
getQuery(FeatureSet, int) - Method in interface com.github.seqware.queryengine.system.exporters.QueryDumperInterface: Return each of the getNumQueries
getQueryInterface() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory: Get a reference to the currently operating Query Interface
getQueue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
getQueue() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
getRandom() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getReadBases() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field readBases.
getReadClass() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field readClass.
getREADCLASS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Gets the value of the readclass property.
getReadCount() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field readCount.
getReader() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread: Getter for the field reader.
getReadIndex() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field readIndex.
getREADINDEX() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Gets the value of the readindex property.
getReadLabel() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field readLabel.
getReadSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field readSpec.
getREADSPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC: Gets the value of the readspec property.
getReadSpecs() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field readSpecs.
getReadsPerSpot() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field readsPerSpot.
getReadsSupportingCallOne() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field readsSupportingCallOne.
getReadsSupportingCallThree() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field readsSupportingCallThree.
getReadsSupportingCallTwo() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field readsSupportingCallTwo.
getReadType() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Getter for the field readType.
getREADTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Gets the value of the readtype property.
getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRun: getReadyToProcess.
getReadyToProcess() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field readyToProcess.
getReference() - Method in class com.github.seqware.queryengine.model.FeatureSet: Get the reference for this featureSet
getReference() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Get the reference for this featureSet
getReference() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Get the reference for this featureSet
getREFERENCEALIGNMENT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the referencealignment property.
getReferenceAveSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field referenceAveSeqQuality.
getReferenceBase() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field referenceBase.
getReferenceCallQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field referenceCallQuality.
getReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getReferenceID() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getReferenceID() - Method in class com.github.seqware.queryengine.model.FeatureSet: Get the referenceID for the associated reference
getReferenceID() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Get the referenceID for the associated reference
getReferenceID() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Get the referenceID for the associated reference
getReferenceId() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field referenceId.
getReferenceIDBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getReferenceIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
getReferenceIDOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getReferenceIDOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
getReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getReferenceIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getReferenceIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getReferenceIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getReferenceIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getReferenceIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getReferenceIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getReferenceIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getReferenceIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getReferenceIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getReferenceIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getReferenceIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getReferenceIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getReferenceIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
getReferenceIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getReferenceIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
getReferenceMaxSeqQuality() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field referenceMaxSeqQuality.
getReferenceName() - Method in class com.github.seqware.queryengine.util.FSGID: Getter for the field referenceName.
getReferences() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: getReferences.
getReferences() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getReferences.
getReferences() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getReferences.
getReferences(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getReferences.
getReferenceSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: getReferenceSets.
getReferenceSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getReferenceSets.
getReferenceSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getReferenceSets.
getReferenceSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getReferenceSets.
getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field refLane.
getRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field refLane.
getRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getRefName() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF: Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF: Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF: Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF: Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR: Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF: Gets the value of the refname property.
getRefname() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF: Gets the value of the refname property.
getRegion() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the region property.
getRegions() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field regions.
getRegions() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field regions.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareFile: Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareLane: Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareSample: Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareStudy: Getter for the field registration.
getRegistration() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Getter for the field registration.
getRegistration(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security: getRegistration.
getRegistrationId() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field registrationId.
getRegistrationService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController: Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController: Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.LoginController: Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController: Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Getter for the field registrationService.
getRegistrationService() - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController: Getter for the field registrationService.
getRegistrationServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getRegistrationServiceBean.
getRelationship() - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Getter for the field relationship.
getRelativeLocation() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field relativeLocation.
getRELEASE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Gets the value of the release property.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.FileReportService: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.FileReportService: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate: getReportForSequencerRun.
getReportForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate: getReportForSequencerRun.
getReportForSequencerRuns(String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO: getReportForSequencerRuns.
getReportForSequencerRuns(String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate: getReportForSequencerRuns.
getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.FileReportService: getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.FileReportService: getReportForStudy.
getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: getReportForStudy.
getReportForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO: getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.FileReportDAO: getReportForStudy.
getReportForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate: getReportForStudy.
getReportForStudy(Study, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileReportDAOHibernate: getReportForStudy.
getRepresentation(Document) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools: getRepresentation.
getRequestedTypeList(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ControllerUtil: getRequestedTypeList.
getRequestedTypeList(HttpServletRequest) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: getRequestedTypeList.
getRequirements() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: get job requirements
getResourceInfo(ApplicationInfo) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
getReturnValue() - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException: Getter for the field returnValue.
getReturnValue() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field returnValue.
getReturnValues() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Getter for the field returnValues.
getRights(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getRights(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getRights(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
getRightsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getRightsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getRightsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
getRightsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getRightsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getRightsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
getRootProcessing(Integer) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: getRootProcessing.
getRootProcessing(Integer) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: getRootProcessing.
getRootProcessing(WorkflowRun) - Static method in class net.sourceforge.solexatools.util.FindChildUtil: getRootProcessing.
getRootProcessingName() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getRootProcessingSwa() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getRootSample(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: getRootSample.
getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService: getRootSample.
getRootSample(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: getRootSample.
getRootSample(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: getRootSample.
getRootSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Getter for the field rootSample.
getRootSamples(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: getRootSamples.
getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.business.SampleService: getRootSamples.
getRootSamples(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: getRootSamples.
getRootSamples(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: getRootSamples.
getRowId() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field rowId.
getRowId() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field rowId.
getRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getRowKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
getRowKey() - Method in class com.github.seqware.queryengine.util.FSGID: Output the portion of the SGID that is used as a rowKey
getRowKey() - Method in class com.github.seqware.queryengine.util.SGID: Output the portion of the SGID that is used as a rowKey
getRows() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Getter for the field rows.
getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getRowsForSequencerRun.
getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getRowsForSequencerRun.
getRowsForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getRowsForSequencerRun.
getRowsForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getRowsForSequencerRun.
getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getRowsWithSequencerRuns.
getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getRowsWithSequencerRuns.
getRowsWithSequencerRuns() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getRowsWithSequencerRuns.
getRowsWithSequencerRuns() - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getRowsWithSequencerRuns.
getRUN() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunSet: Gets the value of the run property.
getRUNATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES: Gets the value of the runattribute property.
getRUNATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the runattributes property.
getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field runCenter.
getRunCenter() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field runCenter.
getRunCenter() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the runCenter property.
getRunDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the runDate property.
getRunFile() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the runFile property.
getRUNLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS: Gets the value of the runlink property.
getRUNLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the runlinks property.
getRunName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getRunningCount(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: getRunningCount.
getRunningCount(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: getRunningCount.
getRUNREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Gets the value of the runref property.
getRunsFromWorkflow(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport: Using a workflow SWID, find all of the workflow runs, and report on each of the workflow runs the files, samples and processing events associated with each.
getRunStartTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field runStartTimestamp.
getRunStartTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field runStartTstmp.
getRunStopTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field runStopTimestamp.
getRunStopTstmp() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field runStopTstmp.
getRunSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getS3InputStream(String, int, long, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: getS3InputStream.
getS3InputStream(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: getS3InputStream.
getS3Url(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: getS3Url.
getS3Url(String, String, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: getS3Url.
getSample() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.SampleAttribute: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.SampleLink: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.SampleSearch: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.ShareSample: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field sample.
getSample() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getSAMPLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleSet: Gets the value of the sample property.
getSample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field sample.
getSample_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field sample_url.
getSAMPLEATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES: Gets the value of the sampleattribute property.
getSampleAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleAttribute: Getter for the field sampleAttributeId.
getSampleAttributes() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field sampleAttributes.
getSAMPLEATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Gets the value of the sampleattributes property.
getSampleCode() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field sampleCode.
getSAMPLEDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Gets the value of the sampledescriptor property.
getSampleHtml(Sample, Registration, String, String, boolean, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getSampleHtml.
getSampleHtml(Sample, Registration, Integer) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getSampleHtml.
getSampleId() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field sampleId.
getSampleId() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field sampleId.
getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER: Gets the value of the sampleId property.
getSampleId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER: Gets the value of the sampleId property.
getSampleId() - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto: Getter for the field sampleId.
getSAMPLELINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS: Gets the value of the samplelink property.
getSampleLinkId() - Method in class net.sourceforge.seqware.common.model.SampleLink: Getter for the field sampleLinkId.
getSampleLinks() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field sampleLinks.
getSAMPLELINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Gets the value of the samplelinks property.
getSampleName() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getSAMPLENAME() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Gets the value of the samplename property.
getSAMPLEPOOLREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Gets the value of the samplepoolref property.
getSAMPLEREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Gets the value of the sampleref property.
getSampleRef() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER: Gets the value of the sampleRef property.
getSampleRef() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER: Gets the value of the sampleRef property.
getSampleReportService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field sampleReportService.
getSampleReportServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getSampleReportServiceBean.
getSamples() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field samples.
getSamples() - Method in class net.sourceforge.seqware.common.model.Lane: getSamples.
getSamples() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field samples.
getSamples() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field samples.
getSamples() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field samples.
getSampleSearch() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: Getter for the field sampleSearch.
getSampleSearchAttributeId() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: Getter for the field sampleSearchAttributeId.
getSampleSearchAttributes() - Method in class net.sourceforge.seqware.common.model.SampleSearch: Getter for the field sampleSearchAttributes.
getSampleSearchId() - Method in class net.sourceforge.seqware.common.model.SampleSearch: Getter for the field sampleSearchId.
getSampleSearchService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field sampleSearchService.
getSampleSearchServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getSampleSearchServiceBean.
getSampleService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.validation.SampleValidator: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Getter for the field sampleService.
getSampleService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController: Getter for the field sampleService.
getSampleServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getSampleServiceBean.
getSampleSwa() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getSampleSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getSampleType() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field sampleType.
getSampleUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto: Getter for the field sampleUrl.
getSchema() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD: Gets the value of the schema property.
getSchema() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE: Gets the value of the schema property.
getScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getScore() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getScore() - Method in class com.github.seqware.queryengine.model.Feature: (GVF: The score of the feature, an integer or floating point number.)
getScore() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field score.
getSector() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the sector property.
getSelectedIds(HttpServletRequest, String, String[], String[]) - Static method in class net.sourceforge.solexatools.util.BulkUtil: getSelectedIds.
getSelectedWorkflowParamValue(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getSelectedWorkflowParamValue.
getSelection() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field selection.
getSender() - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController: Getter for the field sender.
getSeqid() - Method in class com.github.seqware.queryengine.model.Feature: User provided ID for the feature (GVF: The chromosome or contig on which the sequence_alteration is located (text).)
getSequenceOntologyAccession(String) - Static method in class com.github.seqware.queryengine.kernel.Compression: getSequenceOntologyAccession.
getSequenceOntologyAccessionSurrogate(String) - Static method in class com.github.seqware.queryengine.kernel.Compression: Returns the compressed surrogate for a particular SO accession.
getSequencer_run_url() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field sequencer_run_url.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Getter for the field sequencerRun.
getSequencerRun() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getSequencerRun(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil: getSequencerRun.
getSequencerRun(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil: getSequencerRun.
getSequencerRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem: Getter for the field sequencerRun.
getSequencerRunAttributeId() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: Getter for the field sequencerRunAttributeId.
getSequencerRunAttributes() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field sequencerRunAttributes.
getSequencerRunHtml(SequencerRun, Registration, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getSequencerRunHtml.
getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field sequencerRunId.
getSequencerRunId() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field sequencerRunId.
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getSequencerRunReport.
getSequencerRunReport() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getSequencerRunReport.
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getSequencerRunReport.
getSequencerRunReport() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getSequencerRunReport.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun, String, String, int, int) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getSequencerRunReportIds.
getSequencerRunReportIds(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getSequencerRunReportIds.
getSequencerRuns() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field sequencerRuns.
getSequencerRunService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field sequencerRunService.
getSequencerRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Getter for the field sequencerRunService.
getSequencerRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getSequencerRunServiceBean.
getSequencerRunSwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getSequencerRunValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Getter for the field sequencerRunValidator.
getSequencerRunWizardDTO() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: getSequencerRunWizardDTO.
getSequencerRunWizardValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Getter for the field sequencerRunWizardValidator.
getSequencers() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: Getter for the field sequencers.
getSequencers(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: Getter for the field sequencers.
getSequencers() - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: Getter for the field sequencers.
getSequencers(int) - Static method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: Getter for the field sequencers.
getSequencers() - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: Getter for the field sequencers.
getSequencers(int) - Static method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: Getter for the field sequencers.
getSequenceSpace() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field sequenceSpace.
getSEQUENCESPACE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS: Gets the value of the sequencespace property.
getSEQUENCINGPROTOCOL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the sequencingprotocol property.
getSeqwareAccession() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getSeqwareRevision() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field seqwareRevision.
getSeqwareVersion() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field seqwareVersion.
getSerialization() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory: Get a reference to the current operating serialization method
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.ApacheSerialization: Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.KryoSerialization: Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializationConstant() - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization: Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializationConstant() - Method in interface com.github.seqware.queryengine.impl.SerializationInterface: Stored as the first four bytes of serialization so that serialization types can pre-emptively handle their own forward/backward compatibility.
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getSerializedSize() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Lane: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Platform: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Processing: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Project: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Sample: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.Study: Getter for the field serialVersionUID.
getSerialVersionUID() - Static method in class net.sourceforge.seqware.common.model.StudyType: Getter for the field serialVersionUID.
getServer() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field server.
getSessionFactory() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field sessionFactory.
getSessionFactoryBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getSessionFactoryBean.
getSettings() - Static method in class net.sourceforge.seqware.common.util.configtools.ConfigTools: The output keys are always uppercase!
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.factory.Factory: Getter for the field settings.
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.factory.FactoryInterface: getSettings.
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getSettings.
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: Getter for the field settings.
getSettings() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: Getter for the field settings.
getSettings() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: getSettings.
getSETTINGS_MAP() - Static method in class com.github.seqware.queryengine.Constants: Get the settings map.
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
getSGID() - Method in interface com.github.seqware.queryengine.model.Atom: Get the universally unique identifier of this object.
getSGID() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get the universally unique identifier of this object.
getSGID() - Method in class com.github.seqware.queryengine.util.LazyReference: Get the underlying SGID for the lazy reference
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getSgidBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getSgidOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getSgidOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
getSharedStudies() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field sharedStudies.
getSharedWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field sharedWorkflowRuns.
getShareExperimentId() - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Getter for the field shareExperimentId.
getShareFileId() - Method in class net.sourceforge.seqware.common.model.ShareFile: Getter for the field shareFileId.
getShareLaneId() - Method in class net.sourceforge.seqware.common.model.ShareLane: Getter for the field shareLaneId.
getShareProcessingId() - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Getter for the field shareProcessingId.
getShareSampleId() - Method in class net.sourceforge.seqware.common.model.ShareSample: Getter for the field shareSampleId.
getShareStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy: Getter for the field shareStudyId.
getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Getter for the field shareStudyService.
getShareStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Getter for the field shareStudyService.
getShareWorkflowRun(String, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: getShareWorkflowRun.
getShareWorkflowRun(String, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: getShareWorkflowRun.
getShareWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Getter for the field shareWorkflowRunId.
getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Getter for the field shareWorkflowRunService.
getShareWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Getter for the field shareWorkflowRunService.
getSINGLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT: Gets the value of the single property.
getSingleWorkflowRun(Integer) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport: Using a workflow run SWID, report on the files, samples and processing events associated with the run.
getSite() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn: Getter for the field site.
getSize() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field size.
getSize() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getSize() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
getSize() - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Getter for the field size.
getSkip() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field skip.
getSkip() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field skip.
getSkipTxt() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field skipTxt.
getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field slideOneFilePath.
getSlideOneFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field slideOneFilePath.
getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field slideOneLaneCount.
getSlideOneLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field slideOneLaneCount.
getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field slideTwoFilePath.
getSlideTwoFilePath() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field slideTwoFilePath.
getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field slideTwoLaneCount.
getSlideTwoLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field slideTwoLaneCount.
getSortKeySample() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field sortKeySample.
getSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getSource() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getSource() - Method in class com.github.seqware.queryengine.model.Feature: (GVF: The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature.)
getSource() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field source.
getSource() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field source.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD: Gets the value of the source property.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY: Gets the value of the source property.
getSource() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE: Gets the value of the source property.
getSourcePath() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
getSourceReader(String, int, long) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: This attempts to resume if passed in startPosition > 0.
getSPOTDECODEMETHOD() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR: Gets the value of the spotdecodemethod property.
getSPOTDECODESPEC() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR: Gets the value of the spotdecodespec property.
getSPOTDESCRIPTOR() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Gets the value of the spotdescriptor property.
getSpotDesignReadSpec() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field spotDesignReadSpec.
getSql() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Getter for the field sql.
getStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getStart() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getStart() - Method in class com.github.seqware.queryengine.model.Feature: Start coordinate, 0-based (GVF: 1-based integer for the beginning of the sequence_alteration locus on the plus strand (integer))
getStart() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Getter for the field start.
getStartDate() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field startDate.
getStartPage() - Method in class net.sourceforge.solexatools.util.PageInfo: Getter for the field startPage.
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition: Getter for the field startPosition.
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel: Getter for the field startPosition.
getStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field startPosition.
getState(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Accessor method for the back-end.
getState() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
getState(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Accessor method for the back-end.
getState() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field state.
getStats() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Getter for the field stats.
getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getStatus.
getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getStatus.
getStatus(Study, Sample, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getStatus.
getStatus(Study, Sample, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getStatus.
getStatus(Study, Sample, IUS, Lane, SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getStatus.
getStatus() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field status.
getStatus() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field status.
getStatus() - Method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus
getStatusCmd() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field statusCmd.
getStatusCount(Study, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: getStatusCount.
getStatusCount(Study, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: getStatusCount.
getStatusCounts() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools: Getter for the field statusCounts.
getStatuses() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field statuses.
getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getStatusesForSequencerRun.
getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getStatusesForSequencerRun.
getStatusesForSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getStatusesForSequencerRun.
getStatusesForSequencerRun(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getStatusesForSequencerRun.
getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getStatusesForStudy.
getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getStatusesForStudy.
getStatusesForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getStatusesForStudy.
getStatusesForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getStatusesForStudy.
getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getStatusesForWorkflow.
getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getStatusesForWorkflow.
getStatusesForWorkflow(Study, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getStatusesForWorkflow.
getStatusesForWorkflow(Study, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getStatusesForWorkflow.
getStatusesForWorkflow(SequencerRun, Workflow) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getStatusesForWorkflow.
getStderr() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field stderr.
getStdErr() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field stdErr.
getStderr() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field stderr.
getStderrFile() - Method in class net.sourceforge.seqware.pipeline.module.Module: Getter for the file where the stderr will be redirected.
getStdout() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field stdout.
getStdOut() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field stdOut.
getStdout() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field stdout.
getStdoutFile() - Method in class net.sourceforge.seqware.pipeline.module.Module: Getter for the file where the stdout will be redirected.
getStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getStop() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getStop() - Method in class com.github.seqware.queryengine.model.Feature: Stop coordinate, 0-based (GVF: 1-based integer of the end of the sequence_alteration on plus strand (integer).)
getStop() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Getter for the field stop.
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition: Getter for the field stopPosition.
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel: Getter for the field stopPosition.
getStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field stopPosition.
getStorage() - Static method in class com.github.seqware.queryengine.factory.SWQEFactory: Get a reference to the currently operating storage method
getStore(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.factory.Factory: getStore.
getStore(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.factory.FactoryInterface: getStore.
getStore(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.factory.impl.BerkeleyDBFactory: getStore.
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field store.
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Getter for the field store.
getStore() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Getter for the field store.
getStore(String, Long, int) - Static method in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool: getStore.
getStoreType() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field storeType.
getStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getStrand() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getStrand() - Method in class com.github.seqware.queryengine.model.Feature: Strand of the feature.
getStrand() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field strand.
getStrand() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field strand.
getStrategy() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Getter for the field strategy.
getStrExpectedNumberReads() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field strExpectedNumberReads.
getStrExpectedNumberRuns() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field strExpectedNumberRuns.
getStrExpectedNumReads() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field strExpectedNumReads.
getStrExpectedNumRuns() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field strExpectedNumRuns.
getStrLaneCount() - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO: Getter for the field strLaneCount.
getStrRefLane() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field strRefLane.
getStrStartURL() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field strStartURL.
getStrStartURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field strStartURL.
getStudies() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field studies.
getStudy() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.FileReportRow: Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.StudyAttribute: Getter for the field study.
getStudy() - Method in class net.sourceforge.seqware.common.model.StudyLink: Getter for the field study.
getSTUDY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudySet: Gets the value of the study property.
getStudy(Experiment) - Static method in class net.sourceforge.solexatools.util.FindRootUtil: getStudy.
getStudy(Sample) - Static method in class net.sourceforge.solexatools.util.FindRootUtil: getStudy.
getStudy(Lane) - Static method in class net.sourceforge.solexatools.util.FindRootUtil: getStudy.
getStudy(Processing) - Static method in class net.sourceforge.solexatools.util.FindRootUtil: getStudy.
getSTUDYABSTRACT() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Gets the value of the studyabstract property.
getSTUDYATTRIBUTE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES: Gets the value of the studyattribute property.
getStudyAttributeId() - Method in class net.sourceforge.seqware.common.model.StudyAttribute: Getter for the field studyAttributeId.
getStudyAttributes() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field studyAttributes.
getSTUDYATTRIBUTES() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Gets the value of the studyattributes property.
getStudyDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: Getter for the field studyDAO.
getSTUDYDESCRIPTION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Gets the value of the studydescription property.
getStudyId() - Method in class net.sourceforge.seqware.common.model.ShareStudy: Getter for the field studyId.
getStudyId() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field studyId.
getSTUDYLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS: Gets the value of the studylink property.
getStudyLinkId() - Method in class net.sourceforge.seqware.common.model.StudyLink: Getter for the field studyLinkId.
getStudyLinks() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field studyLinks.
getSTUDYLINKS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Gets the value of the studylinks property.
getSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Gets the value of the studyref property.
getSTUDYREF() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the studyref property.
getStudyService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.validation.StudyValidator: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field studyService.
getStudyService() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Getter for the field studyService.
getStudyServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getStudyServiceBean.
getStudySwas() - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
getSTUDYTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Gets the value of the studytitle property.
getStudyType() - Method in class net.sourceforge.seqware.common.model.Lane
getSTUDYTYPE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Gets the value of the studytype property.
getStudyTypeDAO() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: Getter for the field studyTypeDAO.
getStudyTypeId() - Method in class net.sourceforge.seqware.common.model.StudyType: Getter for the field studyTypeId.
getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB
getStudyTypes() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getStudyTypes.
getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection
getStudyTypes() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS
getStudyTypeService() - Method in class net.sourceforge.seqware.common.ContextImpl
getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Getter for the field studyTypeService.
getStudyTypeService() - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController: Getter for the field studyTypeService.
getStudyTypeServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getStudyTypeServiceBean.
getStydyHtml(Study, Registration, String, boolean, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getStydyHtml.
getStydyHtml(Study, Registration, Integer, String) - Static method in class net.sourceforge.solexatools.util.TreeNodeHtmlUtil: getStydyHtml.
getSubject(String, String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos: getSubject.
getSubjectEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams: Getter for the field subjectEmail.
getSUBMISSION() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet: Gets the value of the submission property.
getSubmissionComment() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the submissionComment property.
getSubmissionDate() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the submissionDate property.
getSubmissionId() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the submissionId property.
getSum() - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: Getter for the field sum.
getSummaryData(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getSummaryData.
getSummaryLines() - Method in class net.sourceforge.solexatools.util.SummaryData: Getter for the field summaryLines.
getSUPPRESS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Gets the value of the suppress property.
getSvType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field svType.
getSwa() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field swa.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Invoice: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareFile: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareLane: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareSample: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareStudy: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field swAccession.
getSwAccession() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field swAccession.
getSwCluster() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
getSynonymMap() - Method in class com.github.seqware.queryengine.util.obo.OboParser: Hacked map of terms to synonyms
getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup: getSyntax.
getSyntax() - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator: getSyntax.
getSyntax(OptionParser, String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner: getSyntax.
getTablename() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: getTablename.
getTablename() - Method in class com.github.seqware.queryengine.util.FSGID: getTablename.
getTag() - Method in interface net.sourceforge.seqware.common.model.Attribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.FileAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.IUSAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.SampleAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: Getter for the field tag.
getTag() - Method in class net.sourceforge.seqware.common.model.StudyAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: getTag.
getTag() - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag: Getter for the field tag.
getTag(Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getTag.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE: Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE: Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE: Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE: Gets the value of the tag property.
getTAG() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE: Gets the value of the tag property.
getTagByKey(TagSet, String) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Quickly get the value of a tag by the key.
getTagByKey(String, String) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Quickly get the value of a tag by the key.
getTagByKey(String, String) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable: Quickly get the value of a tag by the key.
getTagByKey(TagSet, String) - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable: Quickly get the value of a tag by the key.
getTagMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getTagMetadata.
getTagMetadata(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getTagMetadata.
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getTags(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getTags(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getTags() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: getTags.
getTags() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getTags.
getTags() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get tags that the implementing class has been tagged with
getTags() - Method in interface com.github.seqware.queryengine.model.interfaces.Taggable: Get tags that the implementing class has been tagged with
getTags() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getTags.
getTags() - Method in class com.github.seqware.queryengine.model.Tag: Get tags that the implementing class has been tagged with
getTags() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field tags.
getTags() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field tags.
getTags() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: the key-value from metadata.xml
getTags() - Method in class net.sourceforge.seqware.queryengine.backend.model.Model: Getter for the field tags.
getTags() - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface: getTags.
getTags() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field tags.
getTags(Integer) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getTags.
getTags(String) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getTags.
getTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getTagsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getTagsBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getTagsBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getTagsCount() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getTagsCount() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getTagsCount() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getTagSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getTagSet() - Method in class com.github.seqware.queryengine.model.Tag: Get a reference to the parent TagSet
getTagSetBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getTagSetIDs() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field tagSetIDs.
getTagSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getTagSetOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getTagSetOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagHierarchicalOccurrence
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagOccurrence
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValue
getTagSetRowKey() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
getTagSets() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: getTagSets.
getTagSets() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getTagSets.
getTagSets() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getTagSets.
getTagSets() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getTagSets.
getTagSetSGID() - Method in class com.github.seqware.queryengine.model.Tag: Get a reference to the parent TagSet
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getTagsList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getTagsList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getTagsList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getTagsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getTagsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getTagsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
getTagsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
getTagsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
getTagsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
getTagSpec(String) - Method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker: Given a key, locate a potential match inside a list of tag sets, otherwise create a new one in the ad hoc set.
getTagSpec() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Getter for the field tagSpec.
getTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getTagSpecIDs(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getTagSpecIDsBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getTagSpecIDsBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getTagSpecIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getTagSpecIDsCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getTagSpecIDsCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getTagSpecIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getTagSpecIDsList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getTagSpecIDsList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getTagSpecIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getTagSpecIDsOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getTagSpecIDsOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getTagSpecIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
getTagSpecIDsOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
getTagSpecIDsOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
getTagValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: getTagValue.
getTagValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: getTagValue.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY: Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE: Gets the value of the target property.
getTarget() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS: Gets the value of the target property.
getTAXONID() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME: Gets the value of the taxonid property.
getTemplate() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field template.
getTemplate() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field template.
getTemplateEmail() - Method in class net.sourceforge.seqware.common.invitation.InvitationParams: Getter for the field templateEmail.
getTemplateFile() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: Getter for the field templateFile.
getTemplatePath() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field templatePath.
getTemplateType() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Getter for the field templateType.
getTerm_name() - Method in enum com.github.seqware.queryengine.Constants.Term
getTermValue(Class<T>) - Method in enum com.github.seqware.queryengine.Constants.Term
getTest() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getTEST_FAMILY_INBYTES() - Static method in class com.github.seqware.queryengine.impl.HBaseStorage: getTEST_FAMILY_INBYTES.
getTestCmd() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field testCmd.
getTests() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
getThickEnd() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field thickEnd.
getThickStart() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field thickStart.
getThreads() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
getThreads() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job
getTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
getTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
getTimestamp() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
getTimestamp() - Method in interface com.github.seqware.queryengine.model.Atom: Get a creation time for this resource.
getTimestamp() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get a creation time for this resource.
getTimeTaken() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field timeTaken.
getTissSource() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Getter for the field tissSource.
getTitle() - Method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header
getTitle() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field title.
getTitle() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field title.
getTitle() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field title.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Gets the value of the title property.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Gets the value of the title property.
getTITLE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Gets the value of the title property.
getTokenNames() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Getter for the field tokenNames.
getTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
getTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
getTombstone() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
getTotal() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Getter for the field total.
getTotalDataBlocks() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Gets the value of the totalDataBlocks property.
getTotalPrice() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field totalPrice.
getTotalPriceString() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field totalPrice.
getTotalReads() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the totalReads property.
getTotalSpots() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Gets the value of the totalSpots property.
getTotalUnits() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field totalUnits.
getTRANSCRIPTASSEMBLY() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the transcriptassembly property.
getTranscriptId() - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Getter for the field transcriptId.
getTRANSCRIPTSEQUENCING() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Gets the value of the transcriptsequencing property.
getTranslatedSequence() - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Getter for the field translatedSequence.
getTranslocationDestinationContig() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field translocationDestinationContig.
getTranslocationDestinationStartPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field translocationDestinationStartPosition.
getTranslocationDestinationStopPosition() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field translocationDestinationStopPosition.
getTranslocationType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field translocationType.
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comment_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comparison_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constant_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constraint_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.high_precedence_constraint_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.identifier_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.key_value_function_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.literal_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.low_precedence_constraint_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.nested_constraint_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.query_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.three_param_predicate_return
getTree() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.two_param_predicate_return
getTreeAdaptor() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: getTreeAdaptor.
getTTL() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Return the expiry date in terms of hours in the future (may fail if the time difference is too large)
getTTL() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable: Return the expiry date in terms of hours in the future (may fail if the time difference is too large)
getType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
getType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
getType() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
getType() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
getType() - Method in class com.github.seqware.queryengine.model.Feature: (From GVF: The type of the feature, this is constrained to be either: (a) the SO term sequence_alteration (SO:0001059), (b) a child term of sequence_alteration, (c) the SO term gap (SO:0000730), or (d) the SO accession number for any of the previous terms.)
getType() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Getter for the field type.
getType() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
getType() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
getType() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field type.
getType() - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Getter for the field type.
getType() - Method in class net.sourceforge.solexatools.webapp.controller.SearchController: Getter for the field type.
getTypeNode() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field typeNode.
getUids(NamingEnumeration<SearchResult>) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication: getUids.
getUniqueDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile: return the unqiue dir associate with the file if the file type is input, the provisioned file will be output to provisionfiles/uniquedir + filename
getUniqueName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
getUniqueName() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
getUnit() - Method in interface net.sourceforge.seqware.common.model.Attribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.FileAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.IUSAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.SampleAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.StudyAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: getUnit.
getUnit() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Getter for the field unit.
getUnits() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.IUSAttribute: Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.SampleAttribute: Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: Getter for the field units.
getUnits() - Method in class net.sourceforge.seqware.common.model.StudyAttribute: Getter for the field units.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE: Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE: Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE: Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE: Gets the value of the units property.
getUNITS() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE: Gets the value of the units property.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Experiment: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Project: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Registration: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Sample: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareStudy: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Study: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field updateTimestamp.
getUpdateTimestamp() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field updateTimestamp.
getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field updateTimeStamp.
getUpdateTimeStamp() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field updateTimeStamp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareFile: Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareLane: Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Getter for the field updateTstmp.
getUpdateTstmp() - Method in class net.sourceforge.seqware.common.model.ShareSample: Getter for the field updateTstmp.
getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field updateValidator.
getUpdateValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: getUpdateValidator.
getUrl() - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.IUSLink: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.LaneLink: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.SampleLink: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.model.StudyLink: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getUrl() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn: Getter for the field url.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK: Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK: Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK: Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK: Gets the value of the url property.
getURL() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK: Gets the value of the url property.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Getter for the field url.
getUrl() - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto: Getter for the field url.
getUrlLabel() - Method in class net.sourceforge.seqware.common.model.File: Getter for the field urlLabel.
getUrlLabel() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field urlLabel.
getUrlLabel() - Method in class net.sourceforge.seqware.common.module.FileMetadata
getUrlLabel() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field urlLabel.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK: Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK: Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK: Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK: Gets the value of the urllink property.
getURLLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK: Gets the value of the urllink property.
getUrlString() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: Getter for the field urlString.
getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRun: Getter for the field useIparIntensities.
getUseIparIntensities() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Getter for the field useIparIntensities.
getUseOneURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field useOneURL.
getUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getUser() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
getUserBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getUsername() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field username.
getUserName() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field userName.
getUsername() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Getter for the field username.
getUserOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
getUserOrBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
getUserOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
getUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getUsers(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getUsers() - Method in class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: Gets all users in all groups
getUsers() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Gets all users in all groups
getUsers() - Method in interface com.github.seqware.queryengine.model.QueryInterface: Gets all users in all groups
getUsers() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getUsers.
getUsersBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getUsersBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getUsersCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getUsersCount() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getUsersCount() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getUsersList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getUsersList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getUsersList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getUsersOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getUsersOrBuilder(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getUsersOrBuilder(int) - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getUsersOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
getUsersOrBuilderList() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
getUsersOrBuilderList() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
getUseTwoURL() - Method in class net.sourceforge.seqware.common.model.UploadSequence: Getter for the field useTwoURL.
getUseURL() - Method in class net.sourceforge.seqware.common.business.UploadFile: Getter for the field useURL.
getUuid() - Method in class com.github.seqware.queryengine.util.SGID: Get underlying UUID implementation, should only be called within the back-end
getVALIDATE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Gets the value of the validate property.
getValidationReportService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field validationReportService.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: getValidator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Getter for the field validator.
getValidator() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Getter for the field validator.
getValue() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Constant
getValue() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValue
getValue() - Method in class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
getValue() - Method in class com.github.seqware.queryengine.model.Tag: Get the value.
getValue() - Method in interface net.sourceforge.seqware.common.model.Attribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.FileAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.IUSAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.SampleAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.StudyAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: getValue.
getValue() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile: Getter for the field value.
getValue() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
getValue() - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag: Getter for the field value.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE: Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE: Gets the value of the value property.
getValue() - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR: Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE: Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE: Gets the value of the value property.
getVALUE() - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE: Gets the value of the value property.
getValue() - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Getter for the field value.
getValueDescriptor() - Method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
getValues() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field values.
getVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVBytes() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVDouble() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getVersion() - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: getVersion.
getVersion() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Get version for the subject
getVersion() - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable: Get version for the subject
getVersion() - Method in interface com.github.seqware.queryengine.model.QueryInterface: getVersion.
getVersion() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.common.module.ReturnValue: Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field version.
getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getVersion() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
getVersion() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: getVersion.
getVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVFloat() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getViewName(String) - Static method in class net.sourceforge.solexatools.util.Constant: getViewName.
getVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVInteger() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getVisibleParams() - Method in class net.sourceforge.solexatools.util.SummaryData: Getter for the field visibleParams.
getVisibleWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow: getVisibleWorkflowParams.
getVisibleWorkflowParamsWithDifferentValue() - Method in class net.sourceforge.seqware.common.model.Workflow: getVisibleWorkflowParamsWithDifferentValue.
getVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVLong() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVSGIDRef() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getVSGIDRefBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVSGIDRefOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVSGIDRefOrBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVSGIDRefOrBuilder() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
getVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
getVString() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
getvType() - Method in class com.github.seqware.queryengine.model.Tag: Get the type of value for the tag value
getWfRuns() - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Getter for the field wfRuns.
getWidth() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
getWorkerName() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Getter for the field workerName.
getWorkerName() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Getter for the field workerName.
getWorkflow() - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field workflow.
getWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getWorkflow_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getWorkflow_run_accession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowAccession.
getWorkflowAccession(String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowAccession.
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowAccession.
getWorkflowAccession(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowAccession.
getWorkflowAccession() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field workflowAccession.
getWorkflowAccession() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getWorkflowAccession(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getWorkflowAccession.
getWorkflowAccessionsToCheck() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
getWorkflowAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: Getter for the field workflowAttributeId.
getWorkflowAttributes() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field workflowAttributes.
getWorkflowBaseDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
getWorkflowBundleDir() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
getWorkflowDataModel() - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory: load metadata.xml, if FTL, parse the FTL to XML, and translate it to Java based Object if Java, load the class.
getWorkflowDir() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Getter for the field workflowDir.
getWorkflowId() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field workflowId.
getWorkflowInfo() - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo: getWorkflowInfo.
getWorkflowMetadata() - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getWorkflowMetadata.
getWorkflowParam() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Getter for the field workflowParam.
getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Getter for the field workflowParamId.
getWorkflowParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Getter for the field workflowParamId.
getWorkflowParamMetadata(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getWorkflowParamMetadata.
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowParams.
getWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowParams.
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowParams.
getWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowParams.
getWorkflowParams() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field workflowParams.
getWorkflowParamService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field workflowParamService.
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Getter for the field workflowParamService.
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController: Getter for the field workflowParamService.
getWorkflowParamService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController: Getter for the field workflowParamService.
getWorkflowParamServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getWorkflowParamServiceBean.
getWorkflowParamsWithDifferentFileMetaType() - Method in class net.sourceforge.seqware.common.model.Workflow: getWorkflowParamsWithDifferentFileMetaType.
getWorkflowParamValueId() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Getter for the field workflowParamValueId.
getWorkflowParamValueService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field workflowParamValueService.
getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Getter for the field workflowParamValueService.
getWorkflowParamValueService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController: Getter for the field workflowParamValueService.
getWorkflowParamValueServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getWorkflowParamValueServiceBean.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field workflowRun.
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowRun.
getWorkflowRun(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowRun.
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowRun.
getWorkflowRun(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Expense: Getter for the field workflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field workflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: Getter for the field workflowRun.
getWorkflowRun() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Getter for the field workflowRun.
getWorkflowRunAccession() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
getWorkflowRunAttributeId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: Getter for the field workflowRunAttributeId.
getWorkflowRunAttributes() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field workflowRunAttributes.
getWorkflowRunByAncestorWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field workflowRunByAncestorWorkflowRunId.
getWorkflowRunHtml(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getWorkflowRunHtml.
getWorkflowRunHtmlWithIUSs(WorkflowRun, Registration, String, String, String) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: getWorkflowRunHtmlWithIUSs.
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.Processing: Getter for the field workflowRunId.
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Getter for the field workflowRunId.
getWorkflowRunId() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field workflowRunId.
getWorkflowRunInfo(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: getWorkflowRunInfo.
getWorkflowRunParam(SortedSet<WorkflowParam>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: getWorkflowRunParam.
getWorkflowRunParamId() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: getWorkflowRunParamId.
getWorkflowRunParams() - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Getter for the field workflowRunParams.
getWorkflowRunProcessings() - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Getter for the field workflowRunProcessings.
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowRunReport.
getWorkflowRunReport(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowRunReport.
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowRunReport.
getWorkflowRunReport(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowRunReport.
getWorkflowRunReport(int, Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowRunReport.
getWorkflowRunReport(Date, Date) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowRunReport.
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.IUS: Getter for the field workflowRuns.
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Lane: Getter for the field workflowRuns.
getWorkflowRuns() - Method in class net.sourceforge.seqware.common.model.Workflow: Getter for the field workflowRuns.
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowRunsByHost.
getWorkflowRunsByHost(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowRunsByHost.
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowRunsByHost.
getWorkflowRunsByHost(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowRunsByHost.
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowRunsByStatus.
getWorkflowRunsByStatus(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowRunsByStatus.
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowRunsByStatus.
getWorkflowRunsByStatus(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowRunsByStatus.
getWorkflowRunService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Getter for the field workflowRunService.
getWorkflowRunService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController: Getter for the field workflowRunService.
getWorkflowRunServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getWorkflowRunServiceBean.
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: getWorkflowRunWithWorkflow.
getWorkflowRunWithWorkflow(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: getWorkflowRunWithWorkflow.
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: getWorkflowRunWithWorkflow.
getWorkflowRunWithWorkflow(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: getWorkflowRunWithWorkflow.
getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getWorkflows.
getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getWorkflows.
getWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getWorkflows.
getWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getWorkflows.
getWorkflowsAndRuns() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
getWorkflowService() - Method in class net.sourceforge.seqware.common.ContextImpl: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController: Getter for the field workflowService.
getWorkflowService() - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController: Getter for the field workflowService.
getWorkflowServiceBean() - Static method in class net.sourceforge.seqware.common.factory.BeanFactory: getWorkflowServiceBean.
getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: getWorkflowsForStudy.
getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.business.SampleReportService: getWorkflowsForStudy.
getWorkflowsForStudy(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate: getWorkflowsForStudy.
getWorkflowsForStudy(Study) - Method in interface net.sourceforge.seqware.common.dao.SampleReportDAO: getWorkflowsForStudy.
getWorkflowSqwVersion() - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: getWorkflowSqwVersion.
getWorkflowsRun() - Method in class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems: getWorkflowsRun.
getWorkflowState(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools: This method examines a Pegasus log directory using the status command provided and will encode the state of the workflow in the ReturnValue object, running as ReturnValue.PROCESSING, failed as ReturnValue.FAILURE, and success as ReturnValue.SUCCESS.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.ExperimentIDFilter: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.OrganismResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.PlatformResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource: getXml.
getXML() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource: getXML.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource: getXml.
getXml() - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource: getXml.
getXREFLINK() - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK: Gets the value of the xreflink property.
getZygosity() - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Getter for the field zygosity.
GFF3_DELETION - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GFF3_DELETION="deletion"
GFF3_INSERTION - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GFF3_INSERTION="insertion"
GFF3_SNV - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GFF3_SNV="VCF_SNV"
GFF3_UNKNOWN_TYPE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GFF3_UNKNOWN_TYPE="unknown_type"
GFF3VariantImportWorker - Class in com.github.seqware.queryengine.system.importers.workers: Ported GFF3VariantImportWorker now using our Hibernate-like entry.
GFF3VariantImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.GFF3VariantImportWorker: Constructor for GFF3VariantImportWorker.
GFF3VariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: GFF3VariantImportWorker class.
GFF3VariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.GFF3VariantImportWorker: Constructor for GFF3VariantImportWorker.
GITest - Class in com.github.seqware.queryengine.tutorial: This is a quick and sample application built on top of our API, created for Poster testing.
GITest(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.GITest: Constructor for GITest.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Expense: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.File: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.IUS: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Lane: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Processing: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Registration: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Sample: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Study: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: givesPermission.
givesPermission(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: givesPermission.
givesPermission(Registration) - Method in interface net.sourceforge.seqware.common.security.PermissionsAware: givesPermission.
grabFeatureListsGivenRow(Result, SGID, SerializationInterface) - Static method in class com.github.seqware.queryengine.impl.HBaseStorage: grabFeatureListsGivenRow.
grabObjectsToBeFlushed() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: grabObjectsToBeFlushed.
Group - Interface in com.github.seqware.queryengine.model: A Group of users that may share ACL permissions
group - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
Group.Builder - Class in com.github.seqware.queryengine.model
Group.Builder() - Constructor for class com.github.seqware.queryengine.model.Group.Builder
GroupIO - Class in com.github.seqware.queryengine.impl.protobufIO: GroupIO class.
GroupIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.GroupIO
GRP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
GRPS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
GT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant GT=11
GT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant GT=11
GTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant GTEQ=12
GTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant GTEQ=12
GVF_ALIAS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_ALIAS="Alias"
GVF_BREAKPOINT_DETAIL - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_BREAKPOINT_DETAIL="Breakpoint_detail"
GVF_DBXREF - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_DBXREF="Dbxref"
GVF_END_RANGE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_END_RANGE="End_range"
GVF_GENOTYPE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_GENOTYPE="Genotype"
GVF_HEMIZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_HEMIZYGOUS="hemizygous"
GVF_HETEROZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_HETEROZYGOUS="heterozygous"
GVF_HOMOZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_HOMOZYGOUS="homozygous"
GVF_INDIVIDUAL - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_INDIVIDUAL="Individual"
GVF_PHASED - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_PHASED="Phased"
GVF_REFERENCE_AA - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_REFERENCE_AA="Reference_aa"
GVF_REFERENCE_CODON - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_REFERENCE_CODON="Reference_codon"
GVF_REFERENCE_SEQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_REFERENCE_SEQ="Reference_seq"
GVF_SEQUENCE_CONTEXT - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_SEQUENCE_CONTEXT="Sequence_context"
GVF_START_RANGE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_START_RANGE="Start_range"
GVF_TOTAL_READS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_TOTAL_READS="Total_reads"
GVF_VARIANT_AA - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_VARIANT_AA="Variant_aa"
GVF_VARIANT_CODON - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_VARIANT_CODON="Variant_codon"
GVF_VARIANT_EFFECT - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_VARIANT_EFFECT="Variant_effect"
GVF_VARIANT_FREQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_VARIANT_FREQ="Variant_freq"
GVF_VARIANT_READS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_VARIANT_READS="Variant_reads"
GVF_VARIANT_SEQ - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_VARIANT_SEQ="Variant_seq"
GVF_ZYGOSITY - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant GVF_ZYGOSITY="Zygosity"

H

HackedPosixParser - Class in org.apache.commons.cli: Workaround for bug with Apache CLI https://issues.apache.org/jira/browse/CLI-185 This can be removed when CLI 1.3 is released
HackedPosixParser() - Constructor for class org.apache.commons.cli.HackedPosixParser
handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
handle(Request, Response) - Method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
handle - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.CycleCheckResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.GenericDBResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource
handle(Request, Response) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource
handle(Callback[]) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler
handleAtom2PB(QESupporting.AtomPB, AtomImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO: Handle serialization of the core atom
handleAtom2PB(QESupporting.FeatureAtomPB, Feature) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO: Handle serialization of the core atom just for Features
handleCancel(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Handles the user's request to delete their study.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Handles the user's request to cancel the lane or the lane update page.
handleCancel(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController: Handles the user's request to cancel.
handleCancel(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Handles the user's request to cancel the lane or the lane update page.
handleCancel(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Handles the user's request to cancel the sequencerRun or the sequencerRun update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Handles the user's request to cancel the registration or the registration update page.
handleCancel(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Handles the user's request to cancel the experiment or the experiment update page.
handleCancel(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Handles the user's request to cancel the experiment or the experiment update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Handles the user's request to cancel the registration or the registration update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Handles the user's request to cancel the study or the study update page.
handleCancel(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Handles the user's request to cancel the registration or the registration update page.
handleCompressedInput(String) - Static method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker: handleCompressedInput.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Handles the user's request to delete their experiment.
handleDelete(HttpServletRequest, HttpServletResponse, File) - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Handles the user's request to delete their file.
handleDelete(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController: Handles the user's request to delete their ius.
handleDelete(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Handles the user's request to delete their lane.
handleDelete(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Handles the user's request to delete their processing.
handleDelete(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Handles the user's request to delete their sample.
handleDelete(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Handles the user's request to delete their study.
handleDelete(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Handles the user's request to delete their study.
handleDeserialization(byte[]) - Static method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin: handleDeserialization.
handleDeserialization(byte[]) - Static method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin: handleDeserialization.
handleGroupByAttribute(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
handleMol2PB(QueryEngine.MoleculePB, MoleculeImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO: This should handle serialization of molecule
handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController: Handles the user's request to submit a new study.
handleNext(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Handles the user's request to submit a new study.
handlePB2Atom(QESupporting.AtomPB, AtomImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO: Handle de-serialization of the core atom
handlePB2Atom(QESupporting.FeatureAtomPB, Feature) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO: Handle de-serialization of the core atom just for Features FIXME: this should be collapsible with normal atom
handlePB2Mol(QueryEngine.MoleculePB, MoleculeImpl) - Static method in class com.github.seqware.queryengine.impl.protobufIO.UtilIO: This should handle de-serialization of molecule
handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController: Handles the user's request to cancel the study or the study update page.
handlePrevious(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Handles the user's request to cancel the study or the study update page.
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AbortLoadIndexPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderSizeValidatorController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelBulkDownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.CancelInputDownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.LogoutController: Handles a user's logout request.
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
handleRequestInternal(HttpServletRequest, HttpServletResponse) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController
handleReset(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Handles the user's request to reset the lane page during a new or update lane.
handleReset(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Handles the user's request to reset the lane page during a new or update lane.
handleReset(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Handles the user's request to reset the sequencerRun page during a new or update sequencerRun.
handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Handles the user's request to reset the registration page during a new or update registration.
handleReset(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Handles the user's request to reset the sample page during a new or update sample.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Handles the user's request to reset the experiment page during a new or update experiment.
handleReset(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Handles the user's request to reset the registration page during a new or update registration.
handleReset(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Handles the user's request to reset the study page during a new or update study.
handleReset(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Handles the user's request to reset the registration page during a new or update registration.
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin: Handle serialization of parameters.
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Handle serialization of parameters.
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin: Handle serialization of parameters.
handleSerialization(Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin: Handle serialization of parameters.
handleShare(HttpServletRequest, HttpServletResponse, WorkflowRun) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Handles the user's request to share their WorkflowRun.
handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Handles the user's request to share their study.
handleShare(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Handles the user's request to share their study.
handleSubmit(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Handles the user's request to submit a new lane.
handleSubmit(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Handles the user's request to submit a new lane.
handleSubmit(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Handles the user's request to submit a new sequencerRun.
handleSubmit(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Handles the user's request to submit a new registration.
handleSubmit(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Handles the user's request to submit a new experiment.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Handles the user's request to submit a new experiment.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Handles the user's request to submit a new registration.
handleSubmit(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, UploadFile) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, UploadSequence) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Handles the user's request to submit a new study.
handleSubmit(HttpServletRequest, HttpServletResponse, SequencerRunWizardDTO) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Handles the user's request to submit a new registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Experiment) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Handles the user's request to update their lane.
handleUpdate(HttpServletRequest, HttpServletResponse, IUS) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController: Handles the user's request to delete their ius.
handleUpdate(HttpServletRequest, HttpServletResponse, Lane) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Handles the user's request to update their lane.
handleUpdate(HttpServletRequest, HttpServletResponse, Processing) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Handles the user's request to update their sequencerRun.
handleUpdate(HttpServletRequest, HttpServletResponse, RegistrationDTO) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Handles the user's request to update their registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Sample) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Handles the user's request to update their experiment.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Handles the user's request to update their experiment.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Handles the user's request to update their registration.
handleUpdate(HttpServletRequest, HttpServletResponse, Study) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, Workflow) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParam) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, WorkflowParamValue) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Handles the user's request to update their study.
handleUpdate(HttpServletRequest, HttpServletResponse, SequencerRun) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Handles the user's request to update their registration.
hasAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
hasAcl() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
hasAcl() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureListPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
hasAtom() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
hasAtom() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
hasCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
hasCascade() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
hasCascade() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
hasDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
hasDate() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
hasDate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
hasDescription() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
hasDescription() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
hasEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
hasEmailAddress() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
hasEmailAddress() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
hasEmailAddressBeenUsed(String) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: hasEmailAddressBeenUsed.
hasEmailAddressBeenUsed(String) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: hasEmailAddressBeenUsed.
hasExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
hasExpiryTime() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
hasExpiryTime() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.MoleculePBOrBuilder
hasFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
hasFeatureSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
hasFeatureSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
hasFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
hasFirstName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
hasFirstName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
hasFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
hasFriendlyRowkey() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
hasFriendlyRowkey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
hasGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
hasGrp() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
hasGrp() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
hashCode() - Method in class com.github.seqware.queryengine.kernel.RPNStack.Parameter
hashCode() - Method in class com.github.seqware.queryengine.model.Feature
hashCode() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
hashCode() - Method in class com.github.seqware.queryengine.model.impl.FeatureList
hashCode() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
hashCode() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
hashCode() - Method in class com.github.seqware.queryengine.model.Tag
hashCode() - Method in class com.github.seqware.queryengine.model.User
hashCode() - Method in class com.github.seqware.queryengine.util.LazyReference
hashCode() - Method in class com.github.seqware.queryengine.util.SGID
hashCode() - Method in class net.sourceforge.seqware.common.model.Expense
hashCode() - Method in class net.sourceforge.seqware.common.model.Experiment
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
hashCode() - Method in class net.sourceforge.seqware.common.model.File
hashCode() - Method in class net.sourceforge.seqware.common.model.FileType
hashCode() - Method in class net.sourceforge.seqware.common.model.Invoice
hashCode() - Method in class net.sourceforge.seqware.common.model.IUS
hashCode() - Method in class net.sourceforge.seqware.common.model.Lane
hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
hashCode() - Method in class net.sourceforge.seqware.common.model.LibrarySource
hashCode() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
hashCode() - Method in class net.sourceforge.seqware.common.model.Organism: hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.Platform
hashCode() - Method in class net.sourceforge.seqware.common.model.Processing
hashCode() - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.Project
hashCode() - Method in class net.sourceforge.seqware.common.model.Registration: hashCode.
hashCode() - Method in class net.sourceforge.seqware.common.model.Sample
hashCode() - Method in class net.sourceforge.seqware.common.model.SampleAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRun
hashCode() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
hashCode() - Method in class net.sourceforge.seqware.common.model.ShareStudy
hashCode() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
hashCode() - Method in class net.sourceforge.seqware.common.model.Study
hashCode() - Method in class net.sourceforge.seqware.common.model.StudyAttribute
hashCode() - Method in class net.sourceforge.seqware.common.model.StudyType
hashCode() - Method in class net.sourceforge.seqware.common.model.Workflow
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
hashCode() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: hashCode.
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument
hashCode() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
hasId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasId() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasId() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
hasLastName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
hasLastName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
hasLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
hasLeastSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
hasLeastSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
hasMetadataWriteback - Variable in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
hasMetadataWriteback() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
hasMetadataWriteback() - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: job specific metadata is not supported yet
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
hasMol() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
hasMol() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
hasMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
hasMostSigBits() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
hasMostSigBits() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
hasName() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
hasName() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.LaneService: hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.ProjectService: hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SampleService: hasNameBeenUsed.
hasNameBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: hasNameBeenUsed.
hasNext() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
hasNext() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
hasNext() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
hasNext() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
hasNext() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
hasNext() - Method in class com.github.seqware.queryengine.util.SeqWareIterator: Super method for dealing with database iterator specifics, such as closing the DB-iterator when no more data is available.
hasNext() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator: hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: hasNext.
hasNext() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: hasNext.
hasNextImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator: Implementation of hasNext().
hasNextImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator: Implementation of hasNext().
hasOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
hasOrganism() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
hasOrganism() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
hasParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
hasParameters() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
hasParameters() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
hasPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
hasPassword() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
hasPassword() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
hasPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasPhase() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasPhase() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasPragma() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasPragma() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
hasPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
hasPrecedingID() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
hasPrecedingID() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.GroupPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferencePBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.TagSetPBOrBuilder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
hasPrecedingVersion() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
hasPrecedingVersion() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.UserPBOrBuilder
hasPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasPredicate() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasPredicate() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
hasReferenceID() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
hasReferenceID() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPBOrBuilder
hasRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
hasRefName() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
hasRefName() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
hasRequiredValues() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
hasRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
hasRowKey() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
hasRowKey() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
hasScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasScore() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasScore() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
hasSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
hasSerializationConstant() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
hasSerializationConstant() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.AtomPBOrBuilder
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPBOrBuilder
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
hasSgid() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
hasSgid() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
hasSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasSource() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasSource() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasStart() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasStart() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasStop() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasStop() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasStrand() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasStrand() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasTagSet() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasTagSet() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
hasTimestamp() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
hasTimestamp() - Method in interface com.github.seqware.queryengine.dto.QESupporting.SGIDPBOrBuilder
hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: hasTitleBeenUsed.
hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: hasTitleBeenUsed.
hasTitleBeenUsed(String, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: hasTitleBeenUsed.
hasTitleBeenUsed(String, String) - Method in interface net.sourceforge.seqware.common.business.StudyService: hasTitleBeenUsed.
hasTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
hasTombstone() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
hasTombstone() - Method in interface com.github.seqware.queryengine.dto.QESupporting.FSGIDPBOrBuilder
hasType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
hasType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
hasType() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.FeaturePBOrBuilder
hasUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
hasUser() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
hasUser() - Method in interface com.github.seqware.queryengine.dto.QueryEngine.ACLPBOrBuilder
hasVariable(String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils: check if a string has FTL style variables ${variable}
hasVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasVBytes() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasVBytes() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasVDouble() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasVDouble() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasVFloat() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasVFloat() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasVInteger() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasVInteger() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasVLong() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasVLong() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasVSGIDRef() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasVSGIDRef() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
hasVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
hasVString() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
hasVString() - Method in interface com.github.seqware.queryengine.dto.QESupporting.TagPBOrBuilder
HBaseModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: FIXME: need to create a locatable model iterator and then pass in the end point, otherwise the code that uses this object will need to do bounds checking!
HBaseModelIterator(ResultScanner, HTable, TupleBinding, String, String, boolean) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: Constructor for HBaseModelIterator.
HBaseModelManager - Class in com.github.seqware.queryengine.impl: A Simple implementation of the CreateUpdateManager interface.
HBaseModelManager() - Constructor for class com.github.seqware.queryengine.impl.HBaseModelManager
HBasePersistentBackEnd - Class in com.github.seqware.queryengine.impl: Implement HBase optimizations for the back-end
HBasePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.HBasePersistentBackEnd: Constructor for HBasePersistentBackEnd.
HBaseRead2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop: HBaseRead2 class.
HBaseRead2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseRead2
HBaseReadWriteExample - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop: HBaseReadWriteExample class.
HBaseReadWriteExample() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseReadWriteExample
HBaseStorage - Class in com.github.seqware.queryengine.impl: HBaseStorage class.
HBaseStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage: Constructor for HBaseStorage.
HBaseStorage.FeatureScanIterable - Class in com.github.seqware.queryengine.impl: A scanner specifically for Features.
HBaseStorage.FeatureScanIterable(ResultScanner, SGID) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterable
HBaseStorage.FeatureScanIterator - Class in com.github.seqware.queryengine.impl: Presents an interface for iterating through FeatureLists
HBaseStorage.FeatureScanIterator(ResultScanner, SGID) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
HBaseStorage.ScanIterable - Class in com.github.seqware.queryengine.impl: A generic scanner
HBaseStorage.ScanIterable(ResultScanner, Class) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
HBaseStorage.ScanIterator - Class in com.github.seqware.queryengine.impl: Presents an interface for iterating through SGIDs
HBaseStorage.ScanIterator(ResultScanner, Class) - Constructor for class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
HBaseStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl: HBaseStore class.
HBaseStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
HBaseTagModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: HBaseTagModelIterator class.
HBaseTagModelIterator(String, ResultScanner, HTable, TupleBinding, String, String) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: Constructor for HBaseTagModelIterator.
helicos - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource: hello.
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource: hello.
hello(int) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource: hello.
HelloWorld - Class in net.sourceforge.seqware.pipeline.modules.examples: This is a hello world module that should give you an idea of how to create a module of your own.
HelloWorld() - Constructor for class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld
HelloWorld - Class in net.sourceforge.seqware.pipeline.plugins: HelloWorld class.
HelloWorld() - Constructor for class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Constructor for HelloWorld.
HEMIZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant HEMIZYGOUS=3
HETEROZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant HETEROZYGOUS=2
HG_19 - Static variable in class com.github.seqware.queryengine.tutorial.Poster: Constant HG_19="hg_19"
HG_19 - Static variable in class com.github.seqware.queryengine.tutorial.PosterSGE: Constant HG_19="hg_19"
hibernateCalls() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions: hibernateCalls.
high_precedence_constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: high_precedence_constraint.
hold - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
holdForPeriod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
holdUntilDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
HOMOZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant HOMOZYGOUS=1
HTMLTagValidator - Class in net.sourceforge.solexatools.util: HTMLTagValidator class.
HTMLTagValidator() - Constructor for class net.sourceforge.solexatools.util.HTMLTagValidator: Constructor for HTMLTagValidator.
hybridassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE

I

ID - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant ID=13
ID - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant ID=13
id - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
id - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
id - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
ID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
identifier() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: identifier.
IllQualStat - Class in net.sourceforge.seqware.pipeline.modules.qc: Basic QC report This module parses quality report from Illumina pipeline (Gerald) Underlying script: sw_module_parseIllQC.pl Necessary programs: perl Expected output: Ill_QC_summary.csv
IllQualStat() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat
illumina - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
Illumina2SRF - Class in net.sourceforge.seqware.pipeline.modules.io: This module takes an Illumina Genome Analyzer run folder and converts what it finds there into one SRF per lane.
Illumina2SRF() - Constructor for class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF
impersonate(SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Set the UUID, very dangerous, this should never be called outside of the backend
impersonate(SGID, SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Set the UUID, very dangerous, this should never be called outside of the backend
ImportConstants - Class in com.github.seqware.queryengine.system.importers.workers: Noticed that a few of the file types repeat a lot of information that we might want to store as fields (and are fields in the old prototype).
ImportConstants() - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportConstants
Importer - Class in com.github.seqware.queryengine.system.importers: This looks like a class to control concurrency for multiple ImportWorkers, one per input file
Importer(int) - Constructor for class com.github.seqware.queryengine.system.importers.Importer: Constructor for Importer.
Importer() - Constructor for class com.github.seqware.queryengine.system.importers.Importer: Constructor for Importer.
Importer - Class in net.sourceforge.seqware.queryengine.tools.importers: Importer class.
Importer(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.Importer: Constructor for Importer.
Importer() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.Importer: Constructor for Importer.
ImporterTest - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop: ImporterTest class.
ImporterTest() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest
ImporterTest2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop: ImporterTest2 class.
ImporterTest2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest2
ImportWorker - Class in com.github.seqware.queryengine.system.importers.workers: Base Worker class, looks like a Bean for storing settings about the file to be converted.
ImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Constructor for ImportWorker.
ImportWorker(String, Importer, String, boolean, int, int, float, boolean, int, boolean, boolean, int) - Constructor for class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Constructor for ImportWorker.
ImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: ImportWorker class.
ImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Constructor for ImportWorker.
ImportWorker(String, Importer, Store, String, boolean, int, int, float, boolean, int, boolean, boolean, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Constructor for ImportWorker.
includeCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
includeIndels - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
includeSNV - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
indirectBIMap - Variable in class com.github.seqware.queryengine.impl.StorageInterface: These tables are created on-the-fly with a referenceID appended in order to separate out Features by Reference
info(Object) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.info(Object).
info(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.info(Object,Throwable).
informOnError - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
informOnStatus - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
ini2Map(String, Map<String, String>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: ini2Map.
ini2Map(String, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: ini2Map.
ini2Map(InputStream, Map<String, String>, boolean) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: ini2Map.
ini2RichMap(String, Map<String, Map<String, String>>) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: This is a little different than the ini2Map since it allows us to read ini files where key-value annotations on the key-values appear in comments on the previous line above the current such as: key=bam_inputs:type=file:display=T:display_name=BAM Input(s):file_meta_type=application/bam or key=run_ends:type=pulldown:display=T:display_name=Single or Paired Ends:pulldown_items=Single End|1;Paired End|2 The extra information is used by the Portal and Web Service to display interfaces that let people call the workflows correctly.
iniString2Map(String) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: iniString2Map.
init(FeatureSet, Object...) - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: Initialize this plug-in, this is called once when the plug-in is starting a job
init(FeatureSet, Object...) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Initialize this plug-in, this is called once when the plug-in is starting a job
init(FeatureSet, Object...) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin: Initialize this plug-in, this is called once when the plug-in is starting a job
init(FeatureSet, Object...) - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin: Initialize this plug-in, this is called once when the plug-in is starting a job
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: init.
init(DataSource) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Connect to a database for future use
init(String, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: init.
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: init.
init(String, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: init.
init() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.deciders.AlignmentQualityReportDecider: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
init() - Method in class net.sourceforge.seqware.pipeline.module.Module: init.
init() - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: Module initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Bfast: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.bwa.BWA_0_5_9: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.BWA: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.Flat2TableTranscriptDB: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.AddRGTags: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.BamFilters.ConvertBAMTranscript2Genome: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.examples.echo: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.examples.HelloWorld: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericCommandRunner: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.io.Illumina2SRF: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.Picard: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.adapterCont: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.alignStat: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.BCtrend: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.collectFlags: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.coverageXTranscript: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.geneCoverage: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.GenericQCGenome: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.IllQualStat: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.plotStats: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.QCGenome: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualFilter: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.qualStat: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.qc.uniqRead: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.BAM2Count: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.ExonCountsRPKM: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.GeneCountsRPKM: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateVariantDB: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithCodingConsequence: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.AnnotateWithDbSNP: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.CreateVariantDB: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.queryengine.DumpVariantDB: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.SamTools: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.SNVMix: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.srf2fastq: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles: init.
init() - Method in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles: init.
init() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
init() - Method in class net.sourceforge.seqware.pipeline.plugins.AttributeAnnotator: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.BundleManager: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.CycleChecker: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.FileLinker
init() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
init() - Method in class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter: Plugin initialization code goes here.
init() - Method in class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker: Plugin initialization code goes here.
init(Request) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet: init.
initBinder(HttpServletRequest, ServletRequestDataBinder) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController
InMemoryAnalysisSet - Class in com.github.seqware.queryengine.model.impl.inMemory: An in-memory representation of a AnalysisSet.
InMemoryAnalysisSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet
InMemoryAnalysisSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
InMemoryAnalysisSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
InMemoryFeaturesAllPlugin - Class in com.github.seqware.queryengine.plugins.inmemory: InMemoryFeaturesAllPlugin class.
InMemoryFeaturesAllPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin
InMemoryFeaturesAllPlugin.FeaturesAllFilter - Class in com.github.seqware.queryengine.plugins.inmemory
InMemoryFeaturesAllPlugin.FeaturesAllFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesAllPlugin.FeaturesAllFilter
InMemoryFeaturesByAttributesPlugin - Class in com.github.seqware.queryengine.plugins.inmemory: Generic query implementation over all attributes of a Feature (including additional attributes).
InMemoryFeaturesByAttributesPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin
InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter - Class in com.github.seqware.queryengine.plugins.inmemory
InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter
InMemoryFeaturesByFilterPlugin - Class in com.github.seqware.queryengine.plugins.inmemory: Generic query implementation over all attributes of a Feature using a FeatureFilter.
InMemoryFeaturesByFilterPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin
InMemoryFeaturesByRangePlugin - Class in com.github.seqware.queryengine.plugins.inmemory: Retrieves features based on their chromosomal location.
InMemoryFeaturesByRangePlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin
InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter - Class in com.github.seqware.queryengine.plugins.inmemory
InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByRangePlugin.FeaturesByRangeFilter
InMemoryFeaturesByTagPlugin - Class in com.github.seqware.queryengine.plugins.inmemory: InMemoryFeaturesByTagPlugin class.
InMemoryFeaturesByTagPlugin() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin
InMemoryFeaturesByTagPlugin.FeaturesByTagFilter - Class in com.github.seqware.queryengine.plugins.inmemory
InMemoryFeaturesByTagPlugin.FeaturesByTagFilter() - Constructor for class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByTagPlugin.FeaturesByTagFilter
InMemoryFeatureSet - Class in com.github.seqware.queryengine.model.impl.inMemory: An in-memory representation of a feature set.
InMemoryFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
InMemoryFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
InMemoryGroup - Class in com.github.seqware.queryengine.model.impl.inMemory: An in-memory representation of a group.
InMemoryGroup() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup
InMemoryGroup.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
InMemoryGroup.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
InMemoryIterable<T> - Class in com.github.seqware.queryengine.util: A bit of a hack class, allows us to have getCount as well as iterable
InMemoryIterable(Collection) - Constructor for class com.github.seqware.queryengine.util.InMemoryIterable: Constructor for InMemoryIterable.
InMemoryIterator<T> - Class in com.github.seqware.queryengine.util: An in-memory iterator for unit testing of SeqWareIterator.
InMemoryIterator(Iterator<T>) - Constructor for class com.github.seqware.queryengine.util.InMemoryIterator: Creates a new in-memory SeqWareIterator implementation.
InMemoryQueryFutureImpl<T> - Class in com.github.seqware.queryengine.model.impl.inMemory: InMemoryQueryFutureImpl class.
InMemoryQueryFutureImpl() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Constructor for InMemoryQueryFutureImpl.
InMemoryQueryFutureImpl.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
InMemoryQueryFutureImpl.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl.Builder
InMemoryReference - Class in com.github.seqware.queryengine.model.impl.inMemory: An in-memory representation of a reference.
InMemoryReference() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference: Anonymous constructor
InMemoryReference.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
InMemoryReference.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
InMemoryReferenceSet - Class in com.github.seqware.queryengine.model.impl.inMemory: An in-memory representation of a reference set.
InMemoryReferenceSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet
InMemoryReferenceSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
InMemoryReferenceSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
InMemoryTagSet - Class in com.github.seqware.queryengine.model.impl.inMemory: An in-memory representation of a TagSet.
InMemoryTagSet() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet
InMemoryTagSet.Builder - Class in com.github.seqware.queryengine.model.impl.inMemory
InMemoryTagSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
input - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
INPUT_FILES_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant INPUT_FILES_PARAM='i'
inputFile - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
inputFile - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
inputSet - Variable in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin
inputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: insert.
insert(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: insert.
insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: insert.
insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: insert.
insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService: insert.
insert(File) - Method in interface net.sourceforge.seqware.common.business.FileService: insert.
insert(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService: insert.
insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: insert.
insert(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: insert.
insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: insert.
insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: insert.
insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl: insert.
insert(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: insert.
insert(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: insert.
insert(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: insert.
insert(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: insert.
insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: insert.
insert(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: insert.
insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: insert.
insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl: insert.
insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl: insert.
insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl: insert.
insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl: insert.
insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl: insert.
insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl: insert.
insert(SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: insert.
insert(Registration, SequencerRun, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: insert.
insert(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: insert.
insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl: insert.
insert(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: insert.
insert(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: insert.
insert(String[], InvitationParams, MailSender) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: insert.
insert(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: insert.
insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: insert.
insert(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: insert.
insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: This is being used to create a new SequencerRun object and the correct number of assocated Lanes
insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: insert.
insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: insert.
insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: insert.
insert(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: insert.
insert(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: insert.
insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: insert.
insert(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: insert.
insert(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: insert.
insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: insert.
insert(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: insert.
insert(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: insert.
insert(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: insert.
insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: insert.
insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: insert.
insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: insert.
insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: insert.
insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: Inserts a new WorkflowRun and returns its sw_accession number.
insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: insert.
insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: insert.
insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: insert.
insert(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: insert.
insert(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: insert.
insert(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService: insert.
insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService: insert.
insert(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService: insert.
insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService: insert.
insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService: insert.
insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService: insert.
insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService: insert.
insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService: insert.
insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService: insert.
insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService: insert.
insert(SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: insert.
insert(Registration, SequencerRun, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: insert.
insert(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: insert.
insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService: insert.
insert(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService: insert.
insert(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: insert.
insert(String[], InvitationParams, MailSender) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: insert.
insert(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService: insert.
insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService: insert.
insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: insert.
insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: insert.
insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: insert.
insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: insert.
insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: insert.
insert(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: insert.
insert(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: insert.
insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: insert.
insert(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: insert.
insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: insert.
insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: insert.
insert(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: insert.
insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: insert.
insert(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: insert.
insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: insert.
insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: insert.
insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: insert.
insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: insert.
insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: insert.
insert(WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: insert.
insert(Registration, WorkflowRun, SortedSet<WorkflowRunParam>, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: insert.
insert(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: insert.
insert(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO: insert.
insert(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: insert.
insert(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: insert.
insert(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO: insert.
insert(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO: insert.
insert(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO: insert.
insert(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO: insert.
insert(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: insert.
insert(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: insert.
insert(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate: insert.
insert(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: insert.
insert(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: insert.
insert(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate: insert.
insert(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate: insert.
insert(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate: insert.
insert(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate: insert.
insert(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: insert.
insert(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: insert.
insert(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: insert.
insert(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate: insert.
insert(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: insert.
insert(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: insert.
insert(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO: insert.
insert(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate: insert.
insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO: insert.
insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate: insert.
insert(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: insert.
insert(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: insert.
insert(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO: insert.
insert(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate: insert.
insert(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate: insert.
insert(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: insert.
insert(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate: insert.
insert(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate: insert.
insert(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate: insert.
insert(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate: insert.
insert(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate: insert.
insert(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate: insert.
insert(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate: insert.
insert(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: insert.
insert(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate: insert.
insert(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate: insert.
insert(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: insert.
insert(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: insert.
insert(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate: insert.
insert(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: insert.
insert(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: insert.
insert(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: insert.
insert(Registration, SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: insert.
insert(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: insert.
insert(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: insert.
insert(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: insert.
insert(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: insert.
insert(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: insert.
insert(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: insert.
insert(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: insert.
insert(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate: insert.
insert(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: insert.
insert(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: insert.
insert(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate: insert.
insert(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: insert.
insert(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: insert.
insert(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: insert.
insert(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: insert.
insert(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: insert.
insert(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: insert.
insert(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: insert.
insert(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: Inserts a new Invoice and returns its sw_accession number.
insert(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: insert.
insert(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO: insert.
insert(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: insert.
insert(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: insert.
insert(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: insert.
insert(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: insert.
insert(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO: insert.
insert(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: Inserts a new Processing and returns its sw_accession number.
insert(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: insert.
insert(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO: insert.
insert(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO: insert.
insert(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO: insert.
insert(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO: insert.
insert(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO: insert.
insert(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO: insert.
insert(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO: insert.
insert(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO: insert.
insert(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO: insert.
insert(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO: insert.
insert(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: insert.
insert(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: insert.
insert(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO: insert.
insert(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: insert.
insert(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: insert.
insert(SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: insert.
insert(Registration, SequencerRunWizardDTO) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: insert.
insert(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: insert.
insert(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: insert.
insert(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: insert.
insert(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: insert.
insert(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: insert.
insert(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO: insert.
insert(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: insert.
insert(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO: insert.
insert(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: insert.
insert(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: insert.
insert(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO: insert.
insert(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO: insert.
insert(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: Inserts a new Workflow and returns its sw_accession number.
insert(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: insert.
insert(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: Inserts a new WorkflowParam and returns its primary key.
insert(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: insert.
insert(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: Inserts a new WorkflowParamValue and returns its primary key.
insert(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: insert.
insert(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: Inserts a new WorkflowRun and returns its sw_accession number.
insert(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: insert.
insert(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: insert.
insert(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: insert.
InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic
InsertAndReturnNewPrimaryKey(String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: Find out the primary key for the last inserted record FIXME: This is hardcoded for Postgres, need to make DB agnostic
insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: insertFilesAsWorkflowRunParam.
insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: insertFilesAsWorkflowRunParam.
insertFilesAsWorkflowRunParam(WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: insertFilesAsWorkflowRunParam.
insertFilesAsWorkflowRunParam(Registration, WorkflowRun, Map<String, List<File>>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: insertFilesAsWorkflowRunParam.
INSERTION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant INSERTION=2
insertLane(Registration, Sample, UploadSequence, FileType) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: insertLane.
insertLane(Registration, Sample, UploadSequence, FileType) - Method in interface net.sourceforge.seqware.common.business.LaneService: insertLane.
insertWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource: insertWorkflowRun.
InSessionExecutions - Class in net.sourceforge.seqware.common.hibernate: Abstract InSessionExecutions class.
InSessionExecutions() - Constructor for class net.sourceforge.seqware.common.hibernate.InSessionExecutions
installAnalysisPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Install a plug-in so that it can be listed
installAnalysisPlugin(AnalysisPluginInterface) - Method in interface com.github.seqware.queryengine.model.QueryInterface: Install a plug-in so that it can be listed
installBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: installBundle.
installBundle(File, File, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: This method allows you to install the workflow bundle to the metadb optionally building a zip file along the way and archiving it to a safe location.
installBundleDirOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: installBundleDirOnly.
installBundleZipOnly(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: installBundleZipOnly.
instanceOf(Object, String) - Static method in class net.sourceforge.solexatools.util.TagUtils: instanceOf.
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA
instrumentmodel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454
instrumentModel - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
instrumentName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
INT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant INT=14
INT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant INT=14
INT_PARAMETERS - Static variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Constant INT_PARAMETERS="int_parameters"
int_parameters - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper: parameters that will be handled by the plug-in developer but will not be available to the user
IntegerIdComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators: IntegerIdComparator class.
IntegerIdComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.IntegerIdComparator
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
internalGetFieldAccessorTable() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
internalGetValueMap() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
INVALIDARGUMENT - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant INVALIDARGUMENT=9
INVALIDFILE - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant INVALIDFILE=7
INVALIDPARAMETERS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant INVALIDPARAMETERS=2
INVALIDPLUGIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant INVALIDPLUGIN=120
InvitationParams - Class in net.sourceforge.seqware.common.invitation: InvitationParams class.
InvitationParams(String, String, String) - Constructor for class net.sourceforge.seqware.common.invitation.InvitationParams: Constructor for InvitationParams.
InviteNewUserController - Class in net.sourceforge.solexatools.webapp.controller: InviteNewUserController class.
InviteNewUserController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserController: Constructor for InviteNewUserController.
InviteNewUserSetupController - Class in net.sourceforge.solexatools.webapp.controller: InviteNewUserSetupController class.
InviteNewUserSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserSetupController: Constructor for InviteNewUserSetupController.
InviteNewUserValidatorController - Class in net.sourceforge.solexatools.webapp.controller: InviteNewUserValidatorController class.
InviteNewUserValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController: Constructor for InviteNewUserValidatorController.
Invoice - Class in net.sourceforge.seqware.common.model: Invoice class.
Invoice() - Constructor for class net.sourceforge.seqware.common.model.Invoice: Constructor for Invoice.
InvoiceDAO - Interface in net.sourceforge.seqware.common.dao: InvoiceDAO interface.
InvoiceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: InvoiceDAOHibernate class.
InvoiceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: Constructor for InvoiceDAOHibernate.
InvoiceDetailsController - Class in net.sourceforge.solexatools.webapp.controller: InvoiceDetailsController class.
InvoiceDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController: Constructor for InvoiceDetailsController.
InvoiceService - Interface in net.sourceforge.seqware.common.business: InvoiceService interface.
invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController
invoiceService - Variable in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController
InvoiceServiceImpl - Class in net.sourceforge.seqware.common.business.impl: InvoiceServiceImpl class.
InvoiceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: Constructor for InvoiceServiceImpl.
isActiveTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: isActiveTransaction.
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: isActiveTransaction.
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: isActiveTransaction.
isActiveTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: isActiveTransaction.
isActiveTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: isActiveTransaction.
isAuthenticated(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Security: isAuthenticated.
isCheckEmail(String) - Static method in class net.sourceforge.solexatools.validation.LoginValidator: isCheckEmail.
isComplete() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: Non-blocking call to determine whether the result is ready
isComplete() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Non-blocking call to determine whether the result is ready
isComplete() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: Non-blocking call to determine whether the result is ready
isCompressed() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: isCompressed.
isCompressed() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: isCompressed.
isConfigError(Throwable) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos: isConfigError.
isCreateConsequenceAnnotationDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: isCreateConsequenceAnnotationDB.
isCreateCoverageDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: isCreateCoverageDB.
isCreateDbSNPAnnotationDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: isCreateDbSNPAnnotationDB.
isCreateMismatchDB() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: isCreateMismatchDB.
isDebug() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase: isDebug.
isDescendantOf(String) - Method in class com.github.seqware.queryengine.model.Tag: Tests whether the given tag is a parent of this tag -- making this tag a descendant of the parameter tag.
isDisplay() - Method in class net.sourceforge.seqware.common.model.WorkflowParam: isDisplay.
isDone() - Method in class com.github.seqware.queryengine.model.Analysis: Returns true iff the query is ready with its results.
isDone() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Returns true iff the query is ready with its results.
isDone() - Method in interface com.github.seqware.queryengine.model.QueryFuture: Returns true iff the query is ready with its results.
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: isDuplicateFile.
isDuplicateFile(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: isDuplicateFile.
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: isDuplicateFile.
isDuplicateFile(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: isDuplicateFile.
isEnd() - Method in class net.sourceforge.solexatools.util.PageInfo: isEnd.
isExists(String, String) - Method in interface net.sourceforge.seqware.common.business.FileService: isExists.
isExists(String, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: isExists.
isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: isExistsShare.
isExistsShare(Integer, Integer) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: isExistsShare.
isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: isExistsShare.
isExistsShare(Integer, Integer) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: isExistsShare.
isExpires() - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Return true iff this expires
isExpires() - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable: Return true iff this expires
isFinalized() - Method in class net.sourceforge.seqware.common.model.Invoice: isFinalized.
isForceCopy() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
isFullyPaid() - Method in class net.sourceforge.seqware.common.model.Invoice: isFullyPaid.
isGcrSkipIfMissing() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
isGcrSkipIfOutputExists() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.IUSService: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.IUSService: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.LaneService: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.LaneService: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.SampleService: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.SampleService: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.business.StudyService: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: isHasFile.
isHasFile(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: isHasFile.
isHasFile(Integer, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: isHasFile.
isHasFile(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: isHasFile.
isHasFile(Integer, String) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: isHasFile.
isIncludeCoverage() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: isIncludeCoverage.
isIncludeCoverage() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: isIncludeCoverage.
isIncludeIndels() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: isIncludeIndels.
isIncludeIndels() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: isIncludeIndels.
isIncludeIndels() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: isIncludeIndels.
isIncludeSNV() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: isIncludeSNV.
isIncludeSNV() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: isIncludeSNV.
isIncludeSNVs() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: isIncludeSNVs.
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
isInitialized() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
isInput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile: is an input file?
isInstalled() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
isJoinDevelopersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration: isJoinDevelopersMailingList.
isJoinUsersMailingList() - Method in class net.sourceforge.seqware.common.model.Registration: isJoinUsersMailingList.
isLaunch() - Method in class net.sourceforge.seqware.common.model.Workflow: isLaunch.
isLIMSAdmin() - Method in class net.sourceforge.seqware.common.model.Registration: isLIMSAdmin.
isLocked() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock: Deprecated. isLocked.
isMetadataWriteBack() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line
isOutput() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile: is an output file?
isPayee() - Method in class net.sourceforge.seqware.common.model.Registration: isPayee.
isPrivate() - Method in class net.sourceforge.seqware.common.model.Workflow: isPrivate.
isPublic() - Method in class net.sourceforge.seqware.common.model.Workflow: isPublic.
isReadOnly() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: isReadOnly.
isRequireFiles() - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: isRequireFiles.
isReturnIds() - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: isReturnIds.
isSortable() - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
isStart() - Method in class net.sourceforge.solexatools.util.PageInfo: isStart.
isTaskGroup() - Method in class net.sourceforge.seqware.common.model.Processing: isTaskGroup.
isTechnician() - Method in class net.sourceforge.seqware.common.model.Registration: isTechnician.
isTombstone() - Method in class com.github.seqware.queryengine.util.FSGID: Back-end method for Features stored within high capacity featuresets
isUsePairedFile() - Method in class net.sourceforge.seqware.common.model.UploadSequence: isUsePairedFile.
isVerbose() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: isVerbose.
isWait() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: wait for the workflow to finished, user can override this by using --wait from command line
isWorkflowRunAncesstor() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
itemRgb - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
iterator() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterable
iterator() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterable
iterator() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterable
iterator() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
iterator() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet
iterator() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet
iterator() - Method in class com.github.seqware.queryengine.util.InMemoryIterable
iterator() - Method in class com.github.seqware.queryengine.util.SGIDIterable
IUS - Class in net.sourceforge.seqware.common.model
IUS() - Constructor for class net.sourceforge.seqware.common.model.IUS: Constructor for IUS.
IUS_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant IUS_ATTRIBUTES="Header.IUS_ATTRIBUTES.getTitle()"
IUS_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant IUS_PREFIX="ius_"
IUS_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant IUS_SWA="Header.IUS_SWA.getTitle()"
IUS_TAG - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant IUS_TAG="Header.IUS_TAG.getTitle()"
IUS_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant IUS_TAG_PREFIX="Header.IUS_TAG_PREFIX.getTitle()"
IUSAttribute - Class in net.sourceforge.seqware.common.model: IusAttribute generated by hbm2java
IUSAttribute() - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute: Constructor for IUSAttribute.
IUSAttribute(int, IUS) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute: Constructor for IUSAttribute.
IUSAttribute(int, IUS, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSAttribute: Constructor for IUSAttribute.
IUSAttributeDAO - Interface in net.sourceforge.seqware.common.dao: IUSAttributeDAO interface.
IUSAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: IUSAttributeDAOHibernate class.
IUSAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate
IUSController - Class in net.sourceforge.solexatools.webapp.controller: IUSController class.
IUSController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController: Constructor for IUSController.
IUSController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSController: Constructor for IUSController.
IUSDAO - Interface in net.sourceforge.seqware.common.dao: IUSDAO interface.
IUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: IUSDAOHibernate class.
IUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: Constructor for IUSDAOHibernate.
IusDto - Class in net.sourceforge.seqware.webservice.dto
IusDto() - Constructor for class net.sourceforge.seqware.webservice.dto.IusDto
IusFilesResource - Interface in net.sourceforge.seqware.webservice.resources.tables: IusFilesResource interface.
IusFilesServerResource - Class in net.sourceforge.seqware.webservice.resources.tables: IusFilesServerResource class.
IusFilesServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusFilesServerResource: Constructor for IusFilesServerResource.
IusIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: IusIDResource class.
IusIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusIDResource: Constructor for IusIDResource.
IUSLink - Class in net.sourceforge.seqware.common.model: IusLink generated by hbm2java
IUSLink() - Constructor for class net.sourceforge.seqware.common.model.IUSLink: Constructor for IUSLink.
IUSLink(int, IUS, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink: Constructor for IUSLink.
IUSLink(int, IUS, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.IUSLink: Constructor for IUSLink.
IUSLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate: IUSLinkDAO interface.
IUSLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: IUSLinkDAOHibernate class.
IUSLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate
IUSList - Class in net.sourceforge.seqware.common.model.lists: IUSList class.
IUSList() - Constructor for class net.sourceforge.seqware.common.model.lists.IUSList: Constructor for IUSList.
IusResource - Class in net.sourceforge.seqware.webservice.resources.tables: IusResource class.
IusResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusResource: Constructor for IusResource.
IusSearchResource - Interface in net.sourceforge.seqware.webservice.resources.tables: IusSearchResource interface.
IusSearchServerResource - Class in net.sourceforge.seqware.webservice.resources.tables: IusSearchServerResource class.
IusSearchServerResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.IusSearchServerResource: Constructor for IusSearchServerResource.
IUSService - Interface in net.sourceforge.seqware.common.business: IUSService interface.
IUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl: IUSServiceImpl class.
IUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: Constructor for IUSServiceImpl.
IUSSetupController - Class in net.sourceforge.solexatools.webapp.controller: IUSSetupController class.
IUSSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.IUSSetupController

J

JavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
JavaJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JavaJob
JavaSeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
JavaSeqwareModuleJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JavaSeqwareModuleJob
JaxbObject<T> - Class in net.sourceforge.seqware.common.util.xmltools: Convenience class for converting objects into JAXB XML.
JaxbObject() - Constructor for class net.sourceforge.seqware.common.util.xmltools.JaxbObject: JAXB has a memory leak when it comes to making new JAXBContext instances, so one JAXBContext is created for the entire lifetime of the program and initialized with all of the classes that we marshal and unmarshal at the moment, as per the instructions at * http://whileonefork.blogspot.com/2010/09/leaking-of-jaxb.html and * http://jaxb.java.net/guide/Performance_and_thread_safety.html .
jdbcTemplate() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig: jdbcTemplate.
JndiDatasourceCreator - Class in net.sourceforge.seqware.common.util.testtools: JndiDatasourceCreator class.
JndiDatasourceCreator() - Constructor for class net.sourceforge.seqware.common.util.testtools.JndiDatasourceCreator
job - Variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
Job - Interface in net.sourceforge.seqware.pipeline.workflowV2.model
JobModule - Class in net.sourceforge.seqware.pipeline.workflowV2.model: JobModule class.
JobModule(Module) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobModule: Constructor for JobModule.
jobObj - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
JobProfile - Class in net.sourceforge.seqware.pipeline.workflowV2.model: JobProfile class.
JobProfile(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile: Constructor for JobProfile.
JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Constant JSON="json"
JSON - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant JSON="json"
JsonUtil - Class in net.sourceforge.seqware.common.util.jsontools: JsonUtil class.
JsonUtil() - Constructor for class net.sourceforge.seqware.common.util.jsontools.JsonUtil

K

KEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
key_value_function() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: key_value_function.
keyIndex - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
keys() - Method in class net.sourceforge.seqware.pipeline.runner.RunnerParams: keys.
KEYVALUE_OUT_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper: Constant KEYVALUE_OUT_PARAM='k'
keyvalues - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
KryoSerialization - Class in com.github.seqware.queryengine.impl: KryoSerialization class.
KryoSerialization() - Constructor for class com.github.seqware.queryengine.impl.KryoSerialization: Constructor for KryoSerialization.

L

label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
label - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
labName - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
Lane - Class in net.sourceforge.seqware.common.model
Lane() - Constructor for class net.sourceforge.seqware.common.model.Lane: Constructor for Lane.
LANE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant LANE_ATTRIBUTES="Header.LANE_ATTRIBUTES.getTitle()"
LANE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant LANE_NAME="Header.LANE_NAME.getTitle()"
LANE_NUM - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant LANE_NUM="Header.LANE_NUM.getTitle()"
LANE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant LANE_PREFIX="seq_"
LANE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant LANE_SWA="Header.LANE_SWA.getTitle()"
LANE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant LANE_TAG_PREFIX="Header.LANE_TAG_PREFIX.getTitle()"
LaneAttribute - Class in net.sourceforge.seqware.common.model: LaneAttribute generated by hbm2java
LaneAttribute() - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute: Constructor for LaneAttribute.
LaneAttribute(int, Lane) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute: Constructor for LaneAttribute.
LaneAttribute(int, Lane, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneAttribute: Constructor for LaneAttribute.
LaneAttributeDAO - Interface in net.sourceforge.seqware.common.dao.hibernate: LaneAttributeDAO interface.
LaneAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: LaneAttributeDAOHibernate class.
LaneAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate
LaneController - Class in net.sourceforge.solexatools.webapp.controller: LaneController
LaneController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController: Constructor for LaneController.
LaneController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneController: Constructor for LaneController.
LaneDAO - Interface in net.sourceforge.seqware.common.dao: LaneDAO interface.
LaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: LaneDAOHibernate class.
LaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: Constructor for LaneDAOHibernate.
LaneIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: LaneIDResource class.
LaneIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource: Constructor for LaneIDResource.
LaneLink - Class in net.sourceforge.seqware.common.model: LaneLink generated by hbm2java
LaneLink() - Constructor for class net.sourceforge.seqware.common.model.LaneLink: Constructor for LaneLink.
LaneLink(int, Lane, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink: Constructor for LaneLink.
LaneLink(int, Lane, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.LaneLink: Constructor for LaneLink.
LaneLinkDAO - Interface in net.sourceforge.seqware.common.dao.hibernate: LaneLinkDAO interface.
LaneLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: LaneLinkDAOHibernate class.
LaneLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate
LaneList - Class in net.sourceforge.seqware.common.model.lists: LaneList class.
LaneList() - Constructor for class net.sourceforge.seqware.common.model.lists.LaneList: Constructor for LaneList.
LaneResource - Class in net.sourceforge.seqware.webservice.resources.tables: LaneResource class.
LaneResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LaneResource: Constructor for LaneResource.
LaneSampleAssociateController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
LaneSampleAssociateController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: Constructor for LaneSampleAssociateController.
LaneSampleAssociateSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
LaneSampleAssociateSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController: Constructor for LaneSampleAssociateSetupController.
LaneService - Interface in net.sourceforge.seqware.common.business: LaneService interface.
LaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl: LaneServiceImpl class.
LaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: Constructor for LaneServiceImpl.
LaneSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
LaneSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaneSetupController: Constructor for LaneSetupController.
LaneValidator - Class in net.sourceforge.solexatools.validation: LaneValidator class.
LaneValidator() - Constructor for class net.sourceforge.solexatools.validation.LaneValidator: Constructor for LaneValidator.
LASTNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow: launchBundle.
launchBundle(String, String, String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine: launchBundle.
launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow: launchInstalledBundle.
launchInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine: launchInstalledBundle.
launchScheduledBundle(String, String, boolean, boolean) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow: launchScheduledBundle.
launchScheduledBundle(String, String, boolean, boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine: launchScheduledBundle.
launchWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowEngine: launch the workflow according to the info filled in the input objectModel
launchWorkflow(AbstractWorkflowDataModel) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
LaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller: LaunchWorkflowController class.
LaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController: Constructor for LaunchWorkflowController.
LaunchWorkflowListController - Class in net.sourceforge.solexatools.webapp.controller: LaunchWorkflowListController class.
LaunchWorkflowListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController: Constructor for LaunchWorkflowListController.
LaunchWorkflowListDetailsController - Class in net.sourceforge.solexatools.webapp.controller: LaunchWorkflowListDetailsController class.
LaunchWorkflowListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Constructor for LaunchWorkflowListDetailsController.
LaunchWorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller: LaunchWorkflowSetupController class.
LaunchWorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController: Constructor for LaunchWorkflowSetupController.
LaunchWorkflowUtil - Class in net.sourceforge.solexatools.util: LaunchWorkflowUtil class.
LaunchWorkflowUtil() - Constructor for class net.sourceforge.solexatools.util.LaunchWorkflowUtil
LazyFeaturesByAttributesPlugin - Class in com.github.seqware.queryengine.plugins.lazyinmemory: Generic query implementation over all attributes of a Feature (including additional attributes).
LazyFeaturesByAttributesPlugin() - Constructor for class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin
LazyFeatureSet - Class in com.github.seqware.queryengine.model.impl.lazy: An "lazy" representation of a feature set.
LazyFeatureSet() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Creates an in-memory feature set.
LazyFeatureSet.BatchedRowFeatureListsIterator - Class in com.github.seqware.queryengine.model.impl.lazy: Go through the raw iterator from the underlying storage type and batch up the FeatureLists and return them by rows
LazyFeatureSet.BatchedRowFeatureListsIterator() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
LazyFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.lazy
LazyFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
LazyFeatureSet.ConsolidatedFeatureIterator - Class in com.github.seqware.queryengine.model.impl.lazy: Iterates through Features given FeatureLists sorted by rows
LazyFeatureSet.ConsolidatedFeatureIterator() - Constructor for class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
LazyLatestReference<T extends Atom> - Class in com.github.seqware.queryengine.util: Lazy reference class, needed if we wish to reduce the number of random accesses when deserializing objects or creating HBase specific model implementations.
LazyLatestReference(Class<T>) - Constructor for class com.github.seqware.queryengine.util.LazyLatestReference: Constructor for LazyLatestReference.
LazyMolSet<S extends MolSetInterface,T> - Interface in com.github.seqware.queryengine.model.impl: LazyMolSet interface.
LazyReference<T extends Atom> - Class in com.github.seqware.queryengine.util: Lazy reference class, needed if we wish to reduce the number of random accesses when de-serializing objects or creating HBase specific model implementations.
LazyReference(Class<T>) - Constructor for class com.github.seqware.queryengine.util.LazyReference: Constructor for LazyReference.
LEASTSIGBITS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
LibrariesResource - Class in net.sourceforge.seqware.webservice.resources.tables: LibrariesResource class.
LibrariesResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrariesResource: Constructor for LibrariesResource.
libraryconstructionprotocol - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
LibraryDAO - Interface in net.sourceforge.seqware.common.dao: LibraryDAO interface.
LibraryDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
LibraryDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryDAOHibernate
librarydescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
LibraryDto - Class in net.sourceforge.seqware.webservice.dto
LibraryDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryDto
LibraryIdentityDto - Class in net.sourceforge.seqware.webservice.dto
LibraryIdentityDto() - Constructor for class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto
librarylayout - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
libraryname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
LibraryResource - Class in net.sourceforge.seqware.webservice.resources.tables: LibraryResource class.
LibraryResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibraryResource: Constructor for LibraryResource.
LibrarySelection - Class in net.sourceforge.seqware.common.model: LibrarySelection class.
LibrarySelection() - Constructor for class net.sourceforge.seqware.common.model.LibrarySelection: Constructor for LibrarySelection.
libraryselection - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
LibrarySelectionDAO - Interface in net.sourceforge.seqware.common.dao: LibrarySelectionDAO interface.
LibrarySelectionDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: LibrarySelectionDAOHibernate class.
LibrarySelectionDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate: Constructor for LibrarySelectionDAOHibernate.
LibrarySelectionList - Class in net.sourceforge.seqware.common.model.lists: LibrarySelectionList class.
LibrarySelectionList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibrarySelectionList: Constructor for LibrarySelectionList.
LibrarySelectionResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentResource class.
LibrarySelectionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrarySelectionResource: Constructor for ExperimentResource.
LibrarySelectionService - Interface in net.sourceforge.seqware.common.business: LibrarySelectionService interface.
LibrarySelectionServiceImpl - Class in net.sourceforge.seqware.common.business.impl: LibrarySelectionServiceImpl class.
LibrarySelectionServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl: Constructor for LibrarySelectionServiceImpl.
LibraryService - Interface in net.sourceforge.seqware.common.business: LibraryService interface.
LibraryServiceImpl - Class in net.sourceforge.seqware.common.business.impl
LibraryServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryServiceImpl
LibrarySource - Class in net.sourceforge.seqware.common.model: LibrarySource class.
LibrarySource() - Constructor for class net.sourceforge.seqware.common.model.LibrarySource: Constructor for LibrarySource.
librarysource - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
LibrarySourceDAO - Interface in net.sourceforge.seqware.common.dao: LibrarySourceDAO interface.
LibrarySourceDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: LibrarySourceDAOHibernate class.
LibrarySourceDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate: Constructor for LibrarySourceDAOHibernate.
LibrarySourceList - Class in net.sourceforge.seqware.common.model.lists: LibrarySourceList class.
LibrarySourceList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibrarySourceList: Constructor for LibrarySourceList.
LibrarySourceResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentResource class.
LibrarySourceResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibrarySourceResource: Constructor for ExperimentResource.
LibrarySourceService - Interface in net.sourceforge.seqware.common.business: LibrarySourceService interface.
LibrarySourceServiceImpl - Class in net.sourceforge.seqware.common.business.impl: LibrarySourceServiceImpl class.
LibrarySourceServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl: Constructor for LibrarySourceServiceImpl.
LibraryStrategy - Class in net.sourceforge.seqware.common.model: LibraryStrategy class.
LibraryStrategy() - Constructor for class net.sourceforge.seqware.common.model.LibraryStrategy: Constructor for LibraryStrategy.
librarystrategy - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR
LibraryStrategyDAO - Interface in net.sourceforge.seqware.common.dao: LibraryStrategyDAO interface.
LibraryStrategyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: LibraryStrategyDAOHibernate class.
LibraryStrategyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate: Constructor for LibraryStrategyDAOHibernate.
LibraryStrategyList - Class in net.sourceforge.seqware.common.model.lists: LibraryStrategyList class.
LibraryStrategyList() - Constructor for class net.sourceforge.seqware.common.model.lists.LibraryStrategyList: Constructor for LibraryStrategyList.
LibraryStrategyResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentResource class.
LibraryStrategyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.LibraryStrategyResource: Constructor for ExperimentResource.
LibraryStrategyService - Interface in net.sourceforge.seqware.common.business: LibraryStrategyService interface.
LibraryStrategyServiceImpl - Class in net.sourceforge.seqware.common.business.impl: LibraryStrategyServiceImpl class.
LibraryStrategyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl: Constructor for LibraryStrategyServiceImpl.
linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: linkAccessionAndParent.
linkAccessionAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: linkAccessionAndParent.
linkProcessingAndFile(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: linkProcessingAndFile.
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: linkWorkflowRunAndParent.
linkWorkflowRunAndParent(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: linkWorkflowRunAndParent.
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: linkWorkflowRunAndParent.
linkWorkflowRunAndParent(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: linkWorkflowRunAndParent.
linkWorkflowRunAndParent(WorkflowRun, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager: linkWorkflowRunAndParent.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: list.
list(Study) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService: list.
list() - Method in interface net.sourceforge.seqware.common.business.FileService: list.
list() - Method in interface net.sourceforge.seqware.common.business.FileTypeService: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: list.
list(Study) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: list.
list(Registration, String) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: list.
list(List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: list.
list() - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: list.
list(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: list.
list() - Method in interface net.sourceforge.seqware.common.business.InvoiceService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: list.
list(Registration, String) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: list.
list() - Method in interface net.sourceforge.seqware.common.business.IUSService: list.
list(List<Integer>) - Method in interface net.sourceforge.seqware.common.business.LaneService: list.
list() - Method in interface net.sourceforge.seqware.common.business.LaneService: list.
list() - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService: list.
list() - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService: list.
list() - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService: list.
list() - Method in interface net.sourceforge.seqware.common.business.OrganismService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.OrganismService: list.
list() - Method in interface net.sourceforge.seqware.common.business.PlatformService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.PlatformService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ProjectService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.ProjectService: list.
list() - Method in interface net.sourceforge.seqware.common.business.SampleSearchService: list.
list() - Method in interface net.sourceforge.seqware.common.business.SampleService: list.
list() - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareFileService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: list.
list() - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService: list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService: list.
list() - Method in interface net.sourceforge.seqware.common.business.StudyService: list.
list() - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: list.
list() - Method in interface net.sourceforge.seqware.common.business.WorkflowService: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: list.
list(Study) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.FileDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: list.
list(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: list.
list(Registration, String) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: list.
list(List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate: list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: list.
list(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate: list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: list.
list(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: list.
list(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: list.
list() - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: list.
list() - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: list.
list(Registration, String) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: list.
list(List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.SampleSearchDAO: list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO: list.
list(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO: list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: list.
list(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: list.
list(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: list.
list() - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: list.
ListBEDExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters: ListBEDExporter class.
ListBEDExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.ListBEDExporter
listComplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: listComplete.
listComplete() - Method in interface net.sourceforge.seqware.common.business.SampleService: listComplete.
listComplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: listComplete.
listComplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: listComplete.
listFile(Registration, String, List<File>, String[], String[]) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: listFile.
listFile(Registration, String, List<File>, String[], String[]) - Method in interface net.sourceforge.seqware.common.business.LaneService: listFile.
listFilesRecursive(File, ArrayList<File>) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: listFilesRecursive.
listIncomplete() - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: listIncomplete.
listIncomplete() - Method in interface net.sourceforge.seqware.common.business.SampleService: listIncomplete.
listIncomplete() - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: listIncomplete.
listIncomplete() - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: listIncomplete.
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: listInstalledWorkflowParams.
listInstalledWorkflowParams(String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: listInstalledWorkflowParams.
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: listInstalledWorkflowParams.
listInstalledWorkflowParams(String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: listInstalledWorkflowParams.
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: listInstalledWorkflows.
listInstalledWorkflows() - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: listInstalledWorkflows.
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: listInstalledWorkflows.
listInstalledWorkflows() - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: listInstalledWorkflows.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: listMyShared.
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listMyShared.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listMyShared.
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService: listMyShared.
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listMyShared.
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: listMyShared.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: listMyShared.
listMyShared(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: listMyShared.
listMyShared(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: listMyShared.
listMyShared(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: listMyShared.
listMyShared(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: listMyShared.
listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listRelatedWorkflows.
listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listRelatedWorkflows.
listRelatedWorkflows(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: listRelatedWorkflows.
listRelatedWorkflows(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: listRelatedWorkflows.
listRunning(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listRunning.
listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listRunning.
listRunning(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listRunning.
listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listRunning.
listRunning(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: listRunning.
listRunning(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: listRunning.
listSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: listSample.
listSample(Registration) - Method in interface net.sourceforge.seqware.common.business.SampleService: listSample.
listSample(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: listSample.
listSample(Registration) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: listSample.
listSequencerRunsWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: listSequencerRunsWorkflows.
listSequencerRunsWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: listSequencerRunsWorkflows.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: listSharedWithMe.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listSharedWithMe.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.StudyService: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService: listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: listSharedWithMe.
listSharedWithMe(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: listSharedWithMe.
listSharedWithMe(Registration) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: listSharedWithMe.
listSharedWithMe(Registration, Boolean) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: listSharedWithMe.
listSharedWithMeWithSample(Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listSharedWithMeWithSample.
listSharedWithMeWithSample(Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listSharedWithMeWithSample.
listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: listStudyHasFile.
listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.business.StudyService: listStudyHasFile.
listStudyHasFile(Registration, String, Boolean) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: listStudyHasFile.
listStudyHasFile(Registration, String, Boolean) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: listStudyHasFile.
listWithHasFile(SortedSet<Experiment>, String) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: listWithHasFile.
listWithHasFile(SortedSet<Experiment>, String) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: listWithHasFile.
listWithHasFile(SortedSet<IUS>, String) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: listWithHasFile.
listWithHasFile(SortedSet<Lane>, String) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: listWithHasFile.
listWithHasFile(Integer, SortedSet<Sample>, String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: listWithHasFile.
listWithHasFile(List<Study>) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: listWithHasFile.
listWithHasFile(List<Study>, String) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: listWithHasFile.
listWithHasFile(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: listWithHasFile.
listWithHasFile(SortedSet<IUS>, String) - Method in interface net.sourceforge.seqware.common.business.IUSService: listWithHasFile.
listWithHasFile(SortedSet<Lane>, String) - Method in interface net.sourceforge.seqware.common.business.LaneService: listWithHasFile.
listWithHasFile(Integer, SortedSet<Sample>, String) - Method in interface net.sourceforge.seqware.common.business.SampleService: listWithHasFile.
listWithHasFile(List<Study>) - Method in interface net.sourceforge.seqware.common.business.StudyService: listWithHasFile.
listWithHasFile(List<Study>, String) - Method in interface net.sourceforge.seqware.common.business.StudyService: listWithHasFile.
listWithHasFile(List<WorkflowRun>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: listWithHasFile.
listWorkflows(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: listWorkflows.
listWorkflows(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: listWorkflows.
literal() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: literal.
LiveTagResource - Class in net.sourceforge.seqware.queryengine.webservice.view: LiveTagResource class.
LiveTagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.LiveTagResource
LoadIndexPageController - Class in net.sourceforge.solexatools.webapp.controller: LoadIndexPageController class.
LoadIndexPageController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController: Constructor for LoadIndexPageController.
LocatableModel - Class in net.sourceforge.seqware.queryengine.backend.model: LocatableModel class.
LocatableModel() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
LocatableSecondaryCursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: LocatableSecondaryCursorIterator class.
LocatableSecondaryCursorIterator(SecondaryCursor, DatabaseEntry, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator: Constructor for LocatableSecondaryCursorIterator.
LocatableSecondaryCursorIterator(SecondaryCursor, DatabaseEntry, ContigPosition, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator: Constructor for LocatableSecondaryCursorIterator.
locateFile(String) - Method in class net.sourceforge.seqware.common.metadata.Metadata: locateFile.
lockAndAppend(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools: Try to acquire lock.
lockAndAppendLine(File, String) - Static method in class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools: lockAndAppendLine.
LockingFileTools - Class in net.sourceforge.seqware.common.util.filetools.lock: LockingFileTools class.
LockingFileTools() - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.LockingFileTools
Log - Class in net.sourceforge.seqware.common.util: Log class.
LOG - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
log(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase: log.
log(String) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC: log.
log(String) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase: log.
LogAspect - Class in net.sourceforge.seqware.pipeline.runner: This is a test class Created by IntelliJ IDEA.
LogAspect() - Constructor for class net.sourceforge.seqware.pipeline.runner.LogAspect
logging() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig: logging.
LoginController - Class in net.sourceforge.solexatools.webapp.controller: LoginController
LoginController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LoginController: Constructor for LoginController.
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.Authentication: loginSuccess.
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.OICRLdapAuthentication: loginSuccess.
loginSuccess(String, String) - Method in class net.sourceforge.solexatools.authentication.UNCKerberos: loginSuccess.
LoginValidator - Class in net.sourceforge.solexatools.validation: LoginValidator class.
LoginValidator() - Constructor for class net.sourceforge.solexatools.validation.LoginValidator: Constructor for LoginValidator.
LogoutController - Class in net.sourceforge.solexatools.webapp.controller: LogoutController class.
LogoutController() - Constructor for class net.sourceforge.solexatools.webapp.controller.LogoutController: Constructor for LogoutController.
low_precedence_constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: low_precedence_constraint.
ls454 - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM
LT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant LT=15
LT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant LT=15
LTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant LTEQ=16
LTEQ - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant LTEQ=16

M

m2pb(Analysis) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO: Convert from model to protein buffer object
m2pb(AnalysisSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO: Convert from model to protein buffer object
m2pb(Feature) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO: Convert from model to protein buffer object
m2pb(FeatureList) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO: Convert from model to protein buffer object
m2pb(FeatureSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO: Convert from model to protein buffer object
m2pb(FSGID) - Static method in class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO: m2pb.
m2pb(Group) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO: Convert from model to protein buffer object
m2pb(T) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface: Convert from model to protein buffer object
m2pb(Reference) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO: Convert from model to protein buffer object
m2pb(ReferenceSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO: Convert from model to protein buffer object
m2pb(SGID) - Static method in class com.github.seqware.queryengine.impl.protobufIO.SGIDIO: m2pb.
m2pb(Tag) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO: Convert from model to protein buffer object
m2pb(TagSet) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO: Convert from model to protein buffer object
m2pb(Tag) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO: Convert from model to protein buffer object
m2pb(User) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO: Convert from model to protein buffer object
main(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper: Command-line interface
main(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper: main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter: main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.OBOImporter: main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Command-line interface
main(String[]) - Static method in class com.github.seqware.queryengine.system.ReferenceCreator: main.
main(String[]) - Static method in class com.github.seqware.queryengine.system.TagSetCreator: main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.BrianTest: main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.GITest: main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.Poster: main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.PosterSGE: main.
main(String[]) - Static method in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: main.
main(String[]) - Static method in class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup: main.
main(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.module.TestModule: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.modules.examples.MultiEchoTest: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.PluginRunner: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner2: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.ReportTest: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.UnZip: main.
main(String[]) - Static method in class net.sourceforge.seqware.pipeline.tools.Zip: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROC: A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCHBase: A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.examples.CompareDatabasesWithROCOld: A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.BlobReaderWriter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.HBaseRead2: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.ImporterTest2: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest: Main entry point.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2: Main entry point.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.annotators.AnnotateVariantsWithContigAndZygosity: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.BEDExporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.ListBEDExporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.TagDumper: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.TextDumper: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.exporters.WIGExporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.FeatureImporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.PileupCoverageImporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationByPositionImporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationImporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceByPositionImporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceImporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.importers.VariantImporter: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.iterators.CoverageIteratorProcessor: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.iterators.VariantIteratorProcessor: main.
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantAndCoverageDatabases: A simple program that takes a list of posit
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.tools.reporters.CompareTwoVariantDatabases: FIXME: add param to pass in range to compare over eg chr22 or chr1:123-1231231
main(String[]) - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain: main.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.importers.OBOImporter: Import a set of Tag specifications into a new TagSet.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.ReferenceCreator: Create a reference given just a name for the new reference to be created.
mainMethod(String[]) - Static method in class com.github.seqware.queryengine.system.TagSetCreator: Create a reference given just a name for the new reference to be created.
MakeBigWig - Class in net.sourceforge.seqware.pipeline.modules.alignment: Generate bigWig file from a BAM file.
MakeBigWig() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.MakeBigWig
makeReport(String) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport: makeReport.
manageFlushedObjects(List<Map.Entry<String, SimpleModelManager.AtomStatePair>>) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: manageFlushedObjects.
ManageWorkflowsController - Class in net.sourceforge.solexatools.webapp.controller: ManageWorkflowsController class.
ManageWorkflowsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController: Constructor for ManageWorkflowsController.
mAND() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mAND.
manipulateRPNStack(RPNStack, Feature, List<TagSet>, Map<String, Tag>) - Static method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByAttributesPlugin.FeaturesByAttributesFilter
map(Feature, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Mapping implementation that singles out desired atoms into a mapped set.
map(Feature, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin: Mapping implementation that singles out desired atoms into a mapped set.
map(Feature, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin: Mapping implementation that singles out desired atoms into a mapped set.
map(T, S) - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin: Mapping implementation that singles out desired atoms into a mapped set.
mapExpandVariables(Map) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: mapExpandVariables.
mapInit() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: mapInit.
mapInit() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin: mapInit.
mapInit() - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin: mapInit.
mapInit() - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin: mapInit.
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: mapProcessingIdToAccession.
mapProcessingIdToAccession(int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: mapProcessingIdToAccession.
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: mapProcessingIdToAccession.
mapProcessingIdToAccession(int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: mapProcessingIdToAccession.
MapReducePlugin<T extends Atom,S extends MolSetInterface> - Interface in com.github.seqware.queryengine.plugins: An abstracted map-reduce interface.
MapReduceTest - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop: TODO: > iterate over each row and pull out variant objects > check to see if both variants exists at position > if they do then increment counter > write the counter to an hdfs file > need to figure out how to pass parameters to map and reduce classes!
MapReduceTest() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest
MapReduceTest2 - Class in net.sourceforge.seqware.queryengine.prototypes.hadoop: TODO: > iterate over each row and pull out variant objects > check to see if both variants exists at position > if they do then increment counter > write the counter to an hdfs file > need to figure out how to pass parameters to map and reduce classes!
MapReduceTest2() - Constructor for class net.sourceforge.seqware.queryengine.prototypes.hadoop.MapReduceTest2
MapSplice - Class in net.sourceforge.seqware.pipeline.modules.alignment: Align reads with via MapSplice This module launches a MapSplice alignment of given reads file(s) against given reference sequences files.
MapSplice() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.MapSplice
mapString2Int(Map) - Static method in class net.sourceforge.seqware.common.util.maptools.MapTools: mapString2Int.
MapTools - Class in net.sourceforge.seqware.common.util.maptools: MapTools class.
MapTools() - Constructor for class net.sourceforge.seqware.common.util.maptools.MapTools
markDatabaseChanged() - Static method in class net.sourceforge.seqware.common.util.testtools.DatabaseCreator: markDatabaseChanged.
markDatabaseChanged() - Static method in class net.sourceforge.seqware.metadb.util.TestDatabaseCreator: markDatabaseChanged.
marshal(Set<File>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
marshal(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
marshal(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
marshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML
marshal(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject: Turn an object into XML using JAXB and provide the result in a StreamResult.
marshalToDocument(T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject: Turn an object into XML using JAXB and provide the result in a StreamResult.
marshalToDocument(JaxbObject, Object) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools: marshalToDocument.
matchName(String) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl
matchName(String) - Method in interface net.sourceforge.seqware.common.business.SampleService
matchName(String) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: findByName.
matchName(String) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: findByName.
MAX_BASE - Static variable in class com.github.seqware.queryengine.kernel.Compression: Constant MAX_BASE=94
maxCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
maximumMappingQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
maxThreads - Variable in class com.github.seqware.queryengine.system.importers.Importer
maxThreads - Variable in class net.sourceforge.seqware.queryengine.tools.importers.Importer
maxThreads - Static variable in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool: Constant maxThreads=Integer.parseInt(EnvUtil.getProperty("maxconnections"))
MAXVERSIONS - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: Constant MAXVERSIONS=1000
mBRACKET_CLOSE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mBRACKET_CLOSE.
mBRACKET_OPEN() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mBRACKET_OPEN.
mCOMMENT_EOL() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mCOMMENT_EOL.
mCOMMENT_INLINE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mCOMMENT_INLINE.
MD5Generator - Class in net.sourceforge.seqware.common.util: Utility class for calculating MD5 hash on a file's contents.
MD5Generator() - Constructor for class net.sourceforge.seqware.common.util.MD5Generator
md5sum(String) - Method in class net.sourceforge.seqware.common.util.MD5Generator: Returns a 32 character representation of the MD5 hash of the specified file's content.
md5sumFile(String) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: md5sumFile.
member - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF
member - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
members - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
mEQUALS() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mEQUALS.
merge(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: merge.
merge(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: merge.
merge(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: merge.
merge(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: merge.
merge(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: merge.
merge(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: merge.
merge(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: merge.
merge(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: merge.
merge(String, String, Map) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker: merge.
mergeAcl(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
mergeAtom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
mergeAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
mergeFeatureSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
mergeFrom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
mergeFrom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
mergeFrom(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
mergeFrom(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
mergeFrom(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
mergeFrom(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
mergeFrom(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
mergeFrom(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
mergeFrom(QueryEngine.FeatureListPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
mergeFrom(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
mergeFrom(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
mergeFrom(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
mergeFrom(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
mergeFrom(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
mergeFrom(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
mergeFrom(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
mergeFrom(Message) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
mergeFrom(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
mergeGrp(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
mergeMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
mergePrecedingID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
mergePrecedingID(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
mergePrecedingVersion(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
mergePrecedingVersion(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
mergePrecedingVersion(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
mergePrecedingVersion(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
mergePrecedingVersion(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
mergePrecedingVersion(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
mergePrecedingVersion(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
mergePrecedingVersion(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
mergePrecedingVersion(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
mergePrecedingVersion(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
mergeReferenceID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
mergeSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
mergeSgid(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
mergeSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
mergeTagSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
mergeUser(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
mergeVSGIDRef(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
Metadata - Class in net.sourceforge.seqware.common.metadata: Abstract Metadata class.
Metadata() - Constructor for class net.sourceforge.seqware.common.metadata.Metadata
metadata - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
metadata - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
metadata - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
Metadata - Class in net.sourceforge.seqware.pipeline.plugins: This plugin currently lets users creation a limited set of table rows in the database from the command line.
Metadata() - Constructor for class net.sourceforge.seqware.pipeline.plugins.Metadata: Constructor for Metadata.
metadata - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
MetadataDB - Class in net.sourceforge.seqware.common.metadata: MetadataDB class.
MetadataDB() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataDB: Constructor for MetadataDB.
MetadataDB - Class in net.sourceforge.seqware.queryengine.webservice.model: MetadataDB class.
MetadataDB() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB
MetadataInterface - Interface in net.sourceforge.seqware.common.metadata: MetadataInterface interface.
METADATAINVALIDIDCHAIN - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant METADATAINVALIDIDCHAIN=8
MetadataNoConnection - Class in net.sourceforge.seqware.common.metadata: MetadataNoConnection class.
MetadataNoConnection() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataNoConnection
MetadataWS - Class in net.sourceforge.seqware.common.metadata: TODO: this needs to setup rows in experiment_library_design and experiment_spot_design
MetadataWS() - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS: Constructor for MetadataWS.
MetadataWS.LowLevel - Class in net.sourceforge.seqware.common.metadata
MetadataWS.LowLevel(String, String, String) - Constructor for class net.sourceforge.seqware.common.metadata.MetadataWS.LowLevel
metaMap - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
mFLOAT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mFLOAT.
mGT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mGT.
mGTEQ() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mGTEQ.
mID() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mID.
minCoverage - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
minSnpQuality - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
mINT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mINT.
MINUS_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Constant MINUS_STRAND=2
mismatchAAChangeBlosumScore - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mismatchAminoAcidChange - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mismatchChr - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mismatchCodonChange - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mismatchCodonPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
MismatchConsequenceReportProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors: MismatchConsequenceReportProcessor class.
MismatchConsequenceReportProcessor(String, Store, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor: Constructor for MismatchConsequenceReportProcessor.
MismatchConsequenceReportProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor: Constructor for MismatchConsequenceReportProcessor.
MismatchesResource - Class in net.sourceforge.seqware.queryengine.webservice.view: MismatchesResource class.
MismatchesResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.MismatchesResource
mismatchId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
MismatchResource - Class in net.sourceforge.seqware.queryengine.webservice.view: MismatchResource class.
MismatchResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.MismatchResource
mismatchStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mismatchStop - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mismatchType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mLT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mLT.
mLTEQ() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mLTEQ.
mNAMED_CONSTANT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mNAMED_CONSTANT.
mNAMED_FUNCTION() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mNAMED_FUNCTION.
mNAMED_THREE_PARAM_PREDICATE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mNAMED_THREE_PARAM_PREDICATE.
mNAMED_TWO_PARAM_PREDICATE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mNAMED_TWO_PARAM_PREDICATE.
mNOT() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mNOT.
mNOTEQUALS() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mNOTEQUALS.
Model - Class in net.sourceforge.seqware.queryengine.backend.model: Model class.
Model() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Model
ModelInterface - Interface in net.sourceforge.seqware.queryengine.backend.model: ModelInterface interface.
ModelUtil - Class in net.sourceforge.solexatools.util: ModelUtil class.
ModelUtil() - Constructor for class net.sourceforge.solexatools.util.ModelUtil
modify - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
modifyIniFile(String, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
Module - Class in net.sourceforge.seqware.pipeline.module: Abstract Module class.
Module() - Constructor for class net.sourceforge.seqware.pipeline.module.Module
MODULE - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
Module - Enum in net.sourceforge.seqware.pipeline.workflowV2.model: Module class.
ModuleInterface - Interface in net.sourceforge.seqware.pipeline.module: This interface defines the required behavior of a SeqWare module.
ModuleMethod - Enum in net.sourceforge.seqware.pipeline.module: Enumeration class for ModuleMethod Created by IntelliJ IDEA.
ModuleRunner - Class in net.sourceforge.seqware.pipeline.plugins: ModuleRunner class.
ModuleRunner() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ModuleRunner: Constructor for ModuleRunner.
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
MOL_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
Molecule<T extends Molecule> - Interface in com.github.seqware.queryengine.model: Defines core functionality that is shared by classes that are controlled by permissions and are atoms
MoleculeImpl<T extends Molecule> - Class in com.github.seqware.queryengine.model.impl: Implements core functionality that is shared by classes that are controlled by permissions and Versionable, Taggable, TTLable via AtomImpl)
MoleculeImpl() - Constructor for class com.github.seqware.queryengine.model.impl.MoleculeImpl
MolSetInterface<S extends MolSetInterface,T> - Interface in com.github.seqware.queryengine.model.interfaces: Abstracts out some of the semantics for interacting with each of our Set classes.
mOR() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mOR.
MOSTSIGBITS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
MRFeaturesAllPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: Implements the "get all features in a feature set" query
MRFeaturesAllPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesAllPlugin
MRFeaturesByAttributesPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: Implements the tag queries
MRFeaturesByAttributesPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByAttributesPlugin
MRFeaturesByFilterPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: Implements the generic queries which independently decide on whether a Feature is included in a result.
MRFeaturesByFilterPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByFilterPlugin
MRFeaturesByRangePlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: Implements queries by range operations
MRFeaturesByRangePlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByRangePlugin
MRFeaturesByTagsPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: Implements queries by range operations
MRFeaturesByTagsPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByTagsPlugin
MRFeatureSetCountPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: Counts the number of Features in a FeatureSet
MRFeatureSetCountPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin
MRHBaseModelManager - Class in com.github.seqware.queryengine.impl: A Simple implementation of the CreateUpdateManager interface.
MRHBaseModelManager() - Constructor for class com.github.seqware.queryengine.impl.MRHBaseModelManager
MRHBasePersistentBackEnd - Class in com.github.seqware.queryengine.impl: Implement HBase optimizations for the back-end.
MRHBasePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.MRHBasePersistentBackEnd: Constructor for MRHBasePersistentBackEnd.
MRLazyFeatureSet - Class in com.github.seqware.queryengine.model.impl.hbasemrlazy: An "lazy" representation of a feature set.
MRLazyFeatureSet() - Constructor for class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet: Creates an lazy M/R using feature set.
MRLazyFeatureSet.Builder - Class in com.github.seqware.queryengine.model.impl.hbasemrlazy
MRLazyFeatureSet.Builder() - Constructor for class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet.Builder
MRVCFDumperPlugin - Class in com.github.seqware.queryengine.plugins.hbasemr: This plug-in implements a quick and dirty export using Map/Reduce TODO: Copy from HDFS and parse key value file to VCF properly.
MRVCFDumperPlugin() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin
mSTRING() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mSTRING.
mT__26() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mT__26.
mTokens() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mTokens.
MultiEchoTest - Class in net.sourceforge.seqware.pipeline.modules.examples: MultiEchoTest class.
MultiEchoTest() - Constructor for class net.sourceforge.seqware.pipeline.modules.examples.MultiEchoTest
multiplier - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
mutatedGenomicSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mutatedTranslatedSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
mWHITESPACE() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: mWHITESPACE.

N

naiveRun(String[]) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter: Import a set of Features into a particular specified reference.
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: Constant NAME="ExperimentLibraryDesignService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentService: Constant NAME="ExperimentService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: Constant NAME="ExperimentSpotDesignReadSpecService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService: Constant NAME="ExperimentSpotDesignService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileService: Constant NAME="fileService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileTypeService: Constant NAME="FileTypeService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.FileUploadService: Constant NAME="FileUploadService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.InvoiceService: Constant NAME="invoiceService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.IUSService: Constant NAME="IUSService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LaneService: Constant NAME="laneService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySelectionService: Constant NAME="LibrarySelectionService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibrarySourceService: Constant NAME="LibrarySourceService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.LibraryStrategyService: Constant NAME="LibraryStrategyService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.OrganismService: Constant NAME="OrganismService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.PlatformService: Constant NAME="PlatformService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ProcessingService: Constant NAME="processingService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ProjectService: Constant NAME="projectService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.RegistrationService: Constant NAME="registrationService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.SampleService: Constant NAME="sampleService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.SequencerRunService: Constant NAME="SequencerRunService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareStudyService: Constant NAME="shareStudyService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: Constant NAME="shareWorkflowRunService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyService: Constant NAME="StudyService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.StudyTypeService: Constant NAME="StudyTypeService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamService: Constant NAME="workflowParamService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: Constant NAME="WorkflowParamValueService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: Constant NAME="WorkflowRunParamService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowRunService: Constant NAME="WorkflowRunService"
NAME - Static variable in interface net.sourceforge.seqware.common.business.WorkflowService: Constant NAME="WorkflowService"
name - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
name - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
name - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
NAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
NAMED_CONSTANT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant NAMED_CONSTANT=17
NAMED_CONSTANT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant NAMED_CONSTANT=17
NAMED_FUNCTION - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant NAMED_FUNCTION=18
NAMED_FUNCTION - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant NAMED_FUNCTION=18
NAMED_THREE_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant NAMED_THREE_PARAM_PREDICATE=19
NAMED_THREE_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant NAMED_THREE_PARAM_PREDICATE=19
NAMED_TWO_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant NAMED_TWO_PARAM_PREDICATE=20
NAMED_TWO_PARAM_PREDICATE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant NAMED_TWO_PARAM_PREDICATE=20
NAMESPACE - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag
NEGATIVE_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
nested_constraint() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: nested_constraint.
net.sourceforge.seqware.common - package net.sourceforge.seqware.common
net.sourceforge.seqware.common.business - package net.sourceforge.seqware.common.business
net.sourceforge.seqware.common.business.impl - package net.sourceforge.seqware.common.business.impl
net.sourceforge.seqware.common.dao - package net.sourceforge.seqware.common.dao
net.sourceforge.seqware.common.dao.hibernate - package net.sourceforge.seqware.common.dao.hibernate
net.sourceforge.seqware.common.err - package net.sourceforge.seqware.common.err
net.sourceforge.seqware.common.factory - package net.sourceforge.seqware.common.factory
net.sourceforge.seqware.common.hibernate - package net.sourceforge.seqware.common.hibernate
net.sourceforge.seqware.common.hibernate.reports - package net.sourceforge.seqware.common.hibernate.reports
net.sourceforge.seqware.common.invitation - package net.sourceforge.seqware.common.invitation
net.sourceforge.seqware.common.metadata - package net.sourceforge.seqware.common.metadata
net.sourceforge.seqware.common.metadata.ProcessingTaskGroup - package net.sourceforge.seqware.common.metadata.ProcessingTaskGroup
net.sourceforge.seqware.common.model - package net.sourceforge.seqware.common.model
net.sourceforge.seqware.common.model.adapters - package net.sourceforge.seqware.common.model.adapters
net.sourceforge.seqware.common.model.comparator - package net.sourceforge.seqware.common.model.comparator
net.sourceforge.seqware.common.model.lists - package net.sourceforge.seqware.common.model.lists
net.sourceforge.seqware.common.module - package net.sourceforge.seqware.common.module
net.sourceforge.seqware.common.security - package net.sourceforge.seqware.common.security
net.sourceforge.seqware.common.util - package net.sourceforge.seqware.common.util
net.sourceforge.seqware.common.util.configtools - package net.sourceforge.seqware.common.util.configtools
net.sourceforge.seqware.common.util.exceptiontools - package net.sourceforge.seqware.common.util.exceptiontools
net.sourceforge.seqware.common.util.filetools - package net.sourceforge.seqware.common.util.filetools
net.sourceforge.seqware.common.util.filetools.lock - package net.sourceforge.seqware.common.util.filetools.lock
net.sourceforge.seqware.common.util.filetools.validate - package net.sourceforge.seqware.common.util.filetools.validate
net.sourceforge.seqware.common.util.freemarker - package net.sourceforge.seqware.common.util.freemarker
net.sourceforge.seqware.common.util.iotools - package net.sourceforge.seqware.common.util.iotools
net.sourceforge.seqware.common.util.jsontools - package net.sourceforge.seqware.common.util.jsontools
net.sourceforge.seqware.common.util.maptools - package net.sourceforge.seqware.common.util.maptools
net.sourceforge.seqware.common.util.processtools - package net.sourceforge.seqware.common.util.processtools
net.sourceforge.seqware.common.util.processtools.stderr - package net.sourceforge.seqware.common.util.processtools.stderr
net.sourceforge.seqware.common.util.processtools.stdout - package net.sourceforge.seqware.common.util.processtools.stdout
net.sourceforge.seqware.common.util.runtools - package net.sourceforge.seqware.common.util.runtools
net.sourceforge.seqware.common.util.testtools - package net.sourceforge.seqware.common.util.testtools
net.sourceforge.seqware.common.util.workflowtools - package net.sourceforge.seqware.common.util.workflowtools
net.sourceforge.seqware.common.util.xmltools - package net.sourceforge.seqware.common.util.xmltools
net.sourceforge.seqware.metadb.util - package net.sourceforge.seqware.metadb.util
net.sourceforge.seqware.pipeline.bundle - package net.sourceforge.seqware.pipeline.bundle
net.sourceforge.seqware.pipeline.daxgenerator - package net.sourceforge.seqware.pipeline.daxgenerator
net.sourceforge.seqware.pipeline.decider - package net.sourceforge.seqware.pipeline.decider
net.sourceforge.seqware.pipeline.deciders - package net.sourceforge.seqware.pipeline.deciders
net.sourceforge.seqware.pipeline.module - package net.sourceforge.seqware.pipeline.module: This package provides the SeqWare module interface and API, including common code and classes.
net.sourceforge.seqware.pipeline.module.ann - package net.sourceforge.seqware.pipeline.module.ann
net.sourceforge.seqware.pipeline.modules - package net.sourceforge.seqware.pipeline.modules
net.sourceforge.seqware.pipeline.modules.alignment - package net.sourceforge.seqware.pipeline.modules.alignment
net.sourceforge.seqware.pipeline.modules.alignment.bwa - package net.sourceforge.seqware.pipeline.modules.alignment.bwa
net.sourceforge.seqware.pipeline.modules.BamFilters - package net.sourceforge.seqware.pipeline.modules.BamFilters
net.sourceforge.seqware.pipeline.modules.examples - package net.sourceforge.seqware.pipeline.modules.examples
net.sourceforge.seqware.pipeline.modules.io - package net.sourceforge.seqware.pipeline.modules.io
net.sourceforge.seqware.pipeline.modules.qc - package net.sourceforge.seqware.pipeline.modules.qc
net.sourceforge.seqware.pipeline.modules.quantification - package net.sourceforge.seqware.pipeline.modules.quantification
net.sourceforge.seqware.pipeline.modules.queryengine - package net.sourceforge.seqware.pipeline.modules.queryengine
net.sourceforge.seqware.pipeline.modules.utilities - package net.sourceforge.seqware.pipeline.modules.utilities
net.sourceforge.seqware.pipeline.plugin - package net.sourceforge.seqware.pipeline.plugin
net.sourceforge.seqware.pipeline.plugins - package net.sourceforge.seqware.pipeline.plugins
net.sourceforge.seqware.pipeline.plugins.filelinker - package net.sourceforge.seqware.pipeline.plugins.filelinker
net.sourceforge.seqware.pipeline.runner - package net.sourceforge.seqware.pipeline.runner
net.sourceforge.seqware.pipeline.tools - package net.sourceforge.seqware.pipeline.tools
net.sourceforge.seqware.pipeline.workflow - package net.sourceforge.seqware.pipeline.workflow
net.sourceforge.seqware.pipeline.workflowV2 - package net.sourceforge.seqware.pipeline.workflowV2
net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus - package net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object - package net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
net.sourceforge.seqware.pipeline.workflowV2.model - package net.sourceforge.seqware.pipeline.workflowV2.model
net.sourceforge.seqware.queryengine.backend.factory - package net.sourceforge.seqware.queryengine.backend.factory
net.sourceforge.seqware.queryengine.backend.factory.impl - package net.sourceforge.seqware.queryengine.backend.factory.impl
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators
net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders - package net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders
net.sourceforge.seqware.queryengine.backend.model - package net.sourceforge.seqware.queryengine.backend.model
net.sourceforge.seqware.queryengine.backend.store - package net.sourceforge.seqware.queryengine.backend.store
net.sourceforge.seqware.queryengine.backend.store.impl - package net.sourceforge.seqware.queryengine.backend.store.impl
net.sourceforge.seqware.queryengine.backend.util - package net.sourceforge.seqware.queryengine.backend.util
net.sourceforge.seqware.queryengine.backend.util.iterators - package net.sourceforge.seqware.queryengine.backend.util.iterators
net.sourceforge.seqware.queryengine.examples - package net.sourceforge.seqware.queryengine.examples
net.sourceforge.seqware.queryengine.prototypes - package net.sourceforge.seqware.queryengine.prototypes
net.sourceforge.seqware.queryengine.prototypes.hadoop - package net.sourceforge.seqware.queryengine.prototypes.hadoop
net.sourceforge.seqware.queryengine.tools.annotators - package net.sourceforge.seqware.queryengine.tools.annotators
net.sourceforge.seqware.queryengine.tools.exporters - package net.sourceforge.seqware.queryengine.tools.exporters
net.sourceforge.seqware.queryengine.tools.importers - package net.sourceforge.seqware.queryengine.tools.importers
net.sourceforge.seqware.queryengine.tools.importers.workers - package net.sourceforge.seqware.queryengine.tools.importers.workers
net.sourceforge.seqware.queryengine.tools.iterators - package net.sourceforge.seqware.queryengine.tools.iterators
net.sourceforge.seqware.queryengine.tools.iterators.processors - package net.sourceforge.seqware.queryengine.tools.iterators.processors
net.sourceforge.seqware.queryengine.tools.reporters - package net.sourceforge.seqware.queryengine.tools.reporters
net.sourceforge.seqware.queryengine.webservice.controller - package net.sourceforge.seqware.queryengine.webservice.controller
net.sourceforge.seqware.queryengine.webservice.model - package net.sourceforge.seqware.queryengine.webservice.model
net.sourceforge.seqware.queryengine.webservice.security - package net.sourceforge.seqware.queryengine.webservice.security
net.sourceforge.seqware.queryengine.webservice.util - package net.sourceforge.seqware.queryengine.webservice.util
net.sourceforge.seqware.queryengine.webservice.view - package net.sourceforge.seqware.queryengine.webservice.view
net.sourceforge.seqware.webservice.dto - package net.sourceforge.seqware.webservice.dto
net.sourceforge.seqware.webservice.resources - package net.sourceforge.seqware.webservice.resources
net.sourceforge.seqware.webservice.resources.filters - package net.sourceforge.seqware.webservice.resources.filters
net.sourceforge.seqware.webservice.resources.queries - package net.sourceforge.seqware.webservice.resources.queries
net.sourceforge.seqware.webservice.resources.tables - package net.sourceforge.seqware.webservice.resources.tables
net.sourceforge.solexatools - package net.sourceforge.solexatools
net.sourceforge.solexatools.authentication - package net.sourceforge.solexatools.authentication
net.sourceforge.solexatools.util - package net.sourceforge.solexatools.util
net.sourceforge.solexatools.validation - package net.sourceforge.solexatools.validation
net.sourceforge.solexatools.webapp.controller - package net.sourceforge.solexatools.webapp.controller
net.sourceforge.solexatools.webapp.metamodel - package net.sourceforge.solexatools.webapp.metamodel
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
newBuilder(QESupporting.AtomPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
newBuilder(QESupporting.FeatureAtomPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
newBuilder(QESupporting.FSGIDPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
newBuilder(QESupporting.SGIDPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
newBuilder(QESupporting.TagPB) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
newBuilder(QueryEngine.ACLPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
newBuilder(QueryEngine.AnalysisPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
newBuilder(QueryEngine.AnalysisSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
newBuilder(QueryEngine.FeatureListPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
newBuilder(QueryEngine.FeaturePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
newBuilder(QueryEngine.FeatureSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
newBuilder(QueryEngine.GroupPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
newBuilder(QueryEngine.MoleculePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
newBuilder(QueryEngine.ReferencePB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
newBuilder(QueryEngine.ReferenceSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
newBuilder(QueryEngine.TagSetPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
newBuilder() - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
newBuilder(QueryEngine.UserPB) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
newBuilder() - Static method in class com.github.seqware.queryengine.model.Feature: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.FeatureList: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Create a new AnalysisSet builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference: Create a new AnalysisSet builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: newBuilder.
newBuilder() - Static method in class com.github.seqware.queryengine.model.interfaces.ACL: Create a new ACL builder, this is needed to add ne
newBuilder() - Static method in class com.github.seqware.queryengine.model.Tag: Create a new ACL builder
newBuilder() - Static method in class com.github.seqware.queryengine.model.User: Create a new ACL builder
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
newBuilderForType() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
NewSeqwareStyle - Annotation Type in net.sourceforge.seqware.pipeline.module.ann: This Annotation is used to tag a ModuleInterface.
newStudyType - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
newSynonym(Synonym) - Method in class com.github.seqware.queryengine.util.obo.OboFileHandlerHack
next() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
next() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
next() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
next() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
next() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
next() - Method in class com.github.seqware.queryengine.util.SeqWareIterator: Super method for dealing with database iterator specifics, such as closing the DB-iterator when no more data is available.
next() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: next.
next() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: next.
nextId() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: nextId.
nextImpl() - Method in class com.github.seqware.queryengine.util.InMemoryIterator: Implementation of next().
nextImpl() - Method in class com.github.seqware.queryengine.util.SeqWareIterator: Implementation of next().
nextInvitationCode() - Method in class net.sourceforge.seqware.common.invitation.RandomInvitationCode: nextInvitationCode.
nextInvitationCode() - Method in class net.sourceforge.solexatools.util.RandomInvitationCode: nextInvitationCode.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: nextSecondaryKey.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: Not applicable for HBase backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: Not applicable for HBase backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.LocatableSecondaryCursorIterator: nextSecondaryKey.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: Not applicable for Postgres backend.
nextSecondaryKey() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: Used to get the keys in this secondary table as strings (won't work for non string keys!).
nextSecondaryKey() - Method in interface net.sourceforge.seqware.queryengine.backend.util.SeqWareIterator: nextSecondaryKey.
NO_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Constant NO_STRAND=0
NodeHtmlUtil - Class in net.sourceforge.solexatools.util: NodeHtmlUtil class.
NodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.NodeHtmlUtil
NoExitSecurityManager - Class in net.sourceforge.seqware.common.util: Created by IntelliJ IDEA.
NoExitSecurityManager() - Constructor for class net.sourceforge.seqware.common.util.NoExitSecurityManager
nominallength - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
nominalsdev - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
NonPersistentStorage - Class in com.github.seqware.queryengine.impl: Doesn't really store things anywhere, just keeps it in memory.
NonPersistentStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.NonPersistentStorage: Constructor for NonPersistentStorage.
NonPersistentStorage.ByteTypePair - Class in com.github.seqware.queryengine.impl
NonPersistentStorage.ByteTypePair(byte[], Class) - Constructor for class com.github.seqware.queryengine.impl.NonPersistentStorage.ByteTypePair
normalizeOptions(String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner2: normalizeOptions.
NOT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant NOT=21
NOT - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant NOT=21
NOT_STRANDED_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
NOTEQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant NOTEQUALS=22
NOTEQUALS - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant NOTEQUALS=22
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
notes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
NotFoundException - Exception in net.sourceforge.seqware.common.err: NotFoundException class.
NotFoundException() - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException: Constructor for NotFoundException.
NotFoundException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException: Constructor for NotFoundException.
NotFoundException(String) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException: Constructor for NotFoundException.
NotFoundException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.NotFoundException: Constructor for NotFoundException.
NOTIMPLEMENTED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant NOTIMPLEMENTED=-1
NS - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
NULL - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant NULL=-99
NullBeanUtils - Class in net.sourceforge.seqware.common.util: NullBeanUtils class.
NullBeanUtils() - Constructor for class net.sourceforge.seqware.common.util.NullBeanUtils
NULLIZYGOUS - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant NULLIZYGOUS=4
NUMBER_THREADS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant NUMBER_THREADS_PARAM='t'
numberChannels - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
numberoflevels - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
numberofreadsperspot - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC

O

objectCreated(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Called by Atoms when they are successfully created thus becoming dirty, and needing to be written to the database.
objectCreated(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Called by Atoms when they are successfully created thus becoming dirty, and needing to be written to the database.
ObjectFactory - Class in net.sourceforge.seqware.queryengine.webservice.model: This object contains factory methods for each Java content interface and Java element interface generated in the net.sourceforge.seqware.queryengine.webservice.model package.
ObjectFactory() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: net.sourceforge.seqware.queryengine.webservice.model
objectToEntry(Object, TupleOutput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.FeatureTB
objectToEntry(Object, TupleOutput) - Method in class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ConsequenceTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.ContigPositionTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.CoverageTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.FeatureTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
objectToEntry(Object, TupleOutput) - Method in class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
OboFileHandlerHack - Class in com.github.seqware.queryengine.util.obo: The BioJava 1.8.1 package does not seem to handle Synonyms correctly, need to keep track of them separately
OboFileHandlerHack(Ontology) - Constructor for class com.github.seqware.queryengine.util.obo.OboFileHandlerHack: Constructor for OboFileHandlerHack.
OBOImporter - Class in com.github.seqware.queryengine.system.importers: Quick and dirty OBO file importer.
OBOImporter() - Constructor for class com.github.seqware.queryengine.system.importers.OBOImporter: Constructor for OBOImporter.
OboParser - Class in com.github.seqware.queryengine.util.obo: Copied from BioJava 1.8.1 Legacy org.biojava.ontology.io.OboParser
OboParser() - Constructor for class com.github.seqware.queryengine.util.obo.OboParser
OICRLdapAuthentication - Class in net.sourceforge.solexatools.authentication: This authentication plugin allows the SeqWare Portal to authenticate against the Ontario Institute for Cancer Research (OICR) LDAP server.
OICRLdapAuthentication() - Constructor for class net.sourceforge.solexatools.authentication.OICRLdapAuthentication
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: Constant OID=0
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: Constant OID=0
OID - Static variable in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Constant OID=0
OldSeqwareException - Exception in net.sourceforge.seqware.common.err: This exception wraps the old seqware exception code User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 2:38 PM
OldSeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException: Constructor for OldSeqwareException.
OldSeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException: Constructor for OldSeqwareException.
OldSeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException: Constructor for OldSeqwareException.
OldSeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.OldSeqwareException: Constructor for OldSeqwareException.
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController: Handles the user's request to submit a new study.
onSubmit(HttpServletRequest, HttpServletResponse, Object, BindException) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController
OpenInvoiceController - Class in net.sourceforge.solexatools.webapp.controller: OpenInvoiceController class.
OpenInvoiceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController: Constructor for OpenInvoiceController.
OptionParsing - Class in net.sourceforge.seqware.common.util.configtools: Created by IntelliJ IDEA.
OptionParsing() - Constructor for class net.sourceforge.seqware.common.util.configtools.OptionParsing
options - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
options - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
options - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
OR - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant OR=23
OR - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant OR=23
org.apache.commons.cli - package org.apache.commons.cli
Organism - Class in net.sourceforge.seqware.common.model: Organism class.
Organism() - Constructor for class net.sourceforge.seqware.common.model.Organism: Constructor for Organism.
ORGANISM_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
OrganismDAO - Interface in net.sourceforge.seqware.common.dao: OrganismDAO interface.
OrganismDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: OrganismDAOHibernate class.
OrganismDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate: Constructor for OrganismDAOHibernate.
OrganismDto - Class in net.sourceforge.seqware.webservice.dto
OrganismDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OrganismDto
OrganismList - Class in net.sourceforge.seqware.common.model.lists: OrganismList class.
OrganismList() - Constructor for class net.sourceforge.seqware.common.model.lists.OrganismList: Constructor for OrganismList.
OrganismResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentResource class.
OrganismResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.OrganismResource: Constructor for ExperimentResource.
OrganismService - Interface in net.sourceforge.seqware.common.business: OrganismService interface.
OrganismServiceImpl - Class in net.sourceforge.seqware.common.business.impl: OrganismServiceImpl class.
OrganismServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl: Constructor for OrganismServiceImpl.
orientation - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED
originalFileName - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
OUTPUT_FILE_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant OUTPUT_FILE_PARAM='o'
outputDir - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
outputDir - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
outputFeatureInVCF(StringBuffer, Feature) - Static method in class com.github.seqware.queryengine.system.exporters.VCFDumper: outputFeatureInVCF.
OUTPUTFILE_PARAM - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper: Constant OUTPUTFILE_PARAM='o'
outputLogString(boolean, WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource: outputLogString.
outputSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin
outputSize - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
outputZip - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
OwnerDto - Class in net.sourceforge.seqware.webservice.dto
OwnerDto() - Constructor for class net.sourceforge.seqware.webservice.dto.OwnerDto

P

packageBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: packageBundle.
packageBundleToS3(File, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: packageBundleToS3.
PAD - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage: Constant PAD=15
PAD - Static variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: Constant PAD=15
padZeros(int, int) - Static method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: padZeros.
PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant PAGE_NUM="page"
PAGE_NUM - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant PAGE_NUM="page"
PageInfo - Class in net.sourceforge.solexatools.util: PageInfo class.
PageInfo() - Constructor for class net.sourceforge.solexatools.util.PageInfo: Constructor for PageInfo.
PaginationUtil - Class in net.sourceforge.solexatools.util: PaginationUtil class.
PaginationUtil() - Constructor for class net.sourceforge.solexatools.util.PaginationUtil
paired - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
parameters - Variable in class net.sourceforge.seqware.common.module.ReturnValue
PARAMETERS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
params - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
params - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
parent - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
PARENT_SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PARENT_SAMPLE_ATTRIBUTES="Header.PARENT_SAMPLE_ATTRIBUTES.getTitl"{trunked}
PARENT_SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PARENT_SAMPLE_NAME="Header.PARENT_SAMPLE_NAME.getTitle()"
PARENT_SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PARENT_SAMPLE_SWA="Header.PARENT_SAMPLE_SWA.getTitle()"
PARENT_SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PARENT_SAMPLE_TAG_PREFIX="Header.PARENT_SAMPLE_TAG_PREFIX.getTitl"{trunked}
parentAccession - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
parentAccessionFiles - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
parse(String) - Static method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser
parse(String, char) - Static method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerParser
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.decider.Decider: Parameter validation code goes here.
parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: Parameter validation code goes here.
parse_parameters() - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Parameter validation code goes here.
parse_parameters() - Method in class net.sourceforge.seqware.pipeline.plugins.ModuleRunner: parse_parameters.
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseDelimitedFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
parseFrom(ByteString) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(byte[]) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(InputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(CodedInputStream) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
parseFromFile(File) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo: parseFromFile.
parseOBO(BufferedReader, String, String) - Method in class com.github.seqware.queryengine.util.obo.OboParser: Parse a OBO file and return its content as a BioJava Ontology object
parseOption(Object, List<String>) - Static method in class net.sourceforge.seqware.common.util.configtools.OptionParsing: parseOption.
parsePegasusStatus(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools: parsePegasusStatus.
parser - Variable in class net.sourceforge.seqware.pipeline.decider.Decider
parser - Variable in class net.sourceforge.seqware.pipeline.plugin.Plugin
parseSGID(String) - Static method in class com.github.seqware.queryengine.system.Utility: Parse a timestamp-less SGID from a String representation
parseXml(AbstractWorkflowDataModel, String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.WorkflowXmlParser: parse the FTL to XML, and XML to Java
PASSWORD_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
pasteHtmlIntoParentNode(String, String, String, boolean) - Static method in class net.sourceforge.solexatools.util.NodeHtmlUtil: pasteHtmlIntoParentNode.
pb2m(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisIO: Convert from protein buffer object to model
pb2m(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.AnalysisSetIO: Convert from protein buffer object to model
pb2m(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureIO: Convert from protein buffer object to model
pb2m(QueryEngine.FeatureListPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureListIO: Convert from protein buffer object to model
pb2m(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.FeatureSetIO: Convert from protein buffer object to model
pb2m(QESupporting.FSGIDPB) - Static method in class com.github.seqware.queryengine.impl.protobufIO.FSGIDIO: pb2m.
pb2m(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.GroupIO: Convert from protein buffer object to model
pb2m(S) - Method in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface: Convert from protein buffer object to model
pb2m(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO: Convert from protein buffer object to model
pb2m(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO: Convert from protein buffer object to model
pb2m(QESupporting.SGIDPB) - Static method in class com.github.seqware.queryengine.impl.protobufIO.SGIDIO: pb2m.
pb2m(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagIO: Convert from protein buffer object to model
pb2m(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSetIO: Convert from protein buffer object to model
pb2m(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO: Convert from protein buffer object to model
pb2m(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.impl.protobufIO.UserIO: Convert from protein buffer object to model
PegasusJavaJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
PegasusJavaJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaJob
PegasusJavaSeqwareModuleJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
PegasusJavaSeqwareModuleJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJavaSeqwareModuleJob
PegasusJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object: a pegasusjob object and its subclasses match to the element in a dax
PegasusJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
PegasusPerlJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
PegasusPerlJob(AbstractJob, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusPerlJob
PegasusWorkflowEngine - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus
PegasusWorkflowEngine() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.PegasusWorkflowEngine
PENDING - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant PENDING="pending"
PENDING - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider: Constant PENDING="pending"
PENDING - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin: Constant PENDING="pending"
percentage - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
percentage - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
performImport(SGID, int, List<String>, String, boolean, File, List<SGID>, SGID, int, SGID, String) - Static method in class com.github.seqware.queryengine.system.importers.FeatureImporter: This method does the actual work of importing given properly parsed parameters
performInMemoryRun() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: performInMemoryRun.
performInMemoryRun() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractMRInMemoryPlugin: performInMemoryRun.
performInMemoryRun() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractScanInMemoryPlugin: performInMemoryRun.
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: This should be overridden by implementing classes with code that changes from map/reduce to map/reduce
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByFilterPlugin: This should be overridden by implementing classes with code that changes from map/reduce to map/reduce
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin: This should be overridden by implementing classes with code that changes from map/reduce to map/reduce
performVariableInit(String, String, Scan) - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin: This should be overridden by implementing classes with code that changes from map/reduce to map/reduce
PerlJob - Class in net.sourceforge.seqware.pipeline.workflowV2.model
PerlJob(String, String, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.PerlJob
permanentBundleLocation - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
PermissionsAware - Interface in net.sourceforge.seqware.common.security: PermissionsAware interface.
persist(Atom) - Method in interface com.github.seqware.queryengine.factory.CreateUpdateManager: Start managing a Atom that has been dirtied, for example, a Atom returned from a query
persist(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager: Start managing a Atom that has been dirtied, for example, a Atom returned from a query
PERSIST_VERSION_CHAINS - Static variable in interface com.github.seqware.queryengine.impl.protobufIO.ProtobufTransferInterface: Constant PERSIST_VERSION_CHAINS=false
Pfn - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
Pfn() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
PHASE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
Picard - Class in net.sourceforge.seqware.pipeline.modules: Picard class.
Picard() - Constructor for class net.sourceforge.seqware.pipeline.modules.Picard
PileupCoverageImporter - Class in net.sourceforge.seqware.queryengine.tools.importers: PileupCoverageImporter class.
PileupCoverageImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.PileupCoverageImporter
PileupVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: PileupVariantImportWorker class.
PileupVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.PileupVariantImportWorker: Constructor for PileupVariantImportWorker.
Platform - Class in net.sourceforge.seqware.common.model: Platform class.
Platform() - Constructor for class net.sourceforge.seqware.common.model.Platform: Constructor for Platform.
platform - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
PlatformDAO - Interface in net.sourceforge.seqware.common.dao: PlatformDAO interface.
PlatformDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: PlatformDAOHibernate class.
PlatformDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate: Constructor for PlatformDAOHibernate.
PlatformList - Class in net.sourceforge.seqware.common.model.lists: PlatformList class.
PlatformList() - Constructor for class net.sourceforge.seqware.common.model.lists.PlatformList: Constructor for PlatformList.
PlatformResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentResource class.
PlatformResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.PlatformResource: Constructor for ExperimentResource.
PlatformService - Interface in net.sourceforge.seqware.common.business: PlatformService interface.
PlatformServiceImpl - Class in net.sourceforge.seqware.common.business.impl: PlatformServiceImpl class.
PlatformServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl: Constructor for PlatformServiceImpl.
plotStats - Class in net.sourceforge.seqware.pipeline.modules.qc: Depends on qualStat module, parse sample_stat.txt and generates boxplot sample_bxp.png for base calling scores and per base/cycle % nucleotide distribution sample_nt_distr.png Underlying script: /usr/bin/fastq_nucleotide_distribution_graph.sh /usr/bin/fastq_quality_boxplot_graph.sh Dependency: fastx_toolkits from http://hannonlab.cshl.edu/fastx_toolkit/commandline.html Expected output: sample_bxp.png & sample_nt_distr.png *
plotStats() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.plotStats
Plugin - Class in net.sourceforge.seqware.pipeline.plugin: Abstract Plugin class.
Plugin() - Constructor for class net.sourceforge.seqware.pipeline.plugin.Plugin: Constructor for Plugin.
PluginInterface - Interface in net.sourceforge.seqware.pipeline.plugin: PluginInterface interface.
PluginRunner - Class in net.sourceforge.seqware.pipeline.runner: PluginRunner class.
PluginRunner() - Constructor for class net.sourceforge.seqware.pipeline.runner.PluginRunner
PLUS_STRAND - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Constant PLUS_STRAND=1
pmi - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
position - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
position - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
PositionSeparator - Static variable in class com.github.seqware.queryengine.util.FSGID: Constant PositionSeparator=":"
POSITIVE_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
post(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource
Poster - Class in com.github.seqware.queryengine.tutorial: This is a quick and dirty sample application built on top of our API, created for Poster testing.
Poster(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.Poster: Constructor for Poster.
PosterSGE - Class in com.github.seqware.queryengine.tutorial: This is a quick and dirty application built on top of our API, created for Poster testing.
PosterSGE(String[]) - Constructor for class com.github.seqware.queryengine.tutorial.PosterSGE: Constructor for PosterSGE.
PosterStatCompiler - Class in com.github.seqware.queryengine.tutorial: This program compiles information generated by the Poster class.
PosterStatCompiler() - Constructor for class com.github.seqware.queryengine.tutorial.PosterStatCompiler
PostgresModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: An interator on top of the standard Java SQL iterator
PostgresModelIterator(ResultSet, TupleBinding, int, LargeObjectManager) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: Constructor for PostgresModelIterator.
PostgreSQLBulkWriterStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl: PostgreSQLBulkWriterStore class.
PostgreSQLBulkWriterStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore
PostgreSQLStore - Class in net.sourceforge.seqware.queryengine.backend.store.impl: PostgreSQLStore class.
PostgreSQLStore() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore
PostgresTagModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: An interator on top of the standard Java SQL iterator
PostgresTagModelIterator(ResultSet, PostgreSQLStore) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: Constructor for PostgresTagModelIterator.
PostgresVariantModelIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: An interator on top of the standard Java SQL iterator
PostgresVariantModelIterator(ResultSet, PostgreSQLStore) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: Constructor for PostgresVariantModelIterator.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.IusResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource: postJaxb.
postJaxb(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource: postJaxb.
postRun(Representation) - Method in class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter: postRun.
PRAGMA_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
PRECEDINGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
PRECEDINGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
PRECEDINGVERSION_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
PREDICATE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
prefix - Static variable in class com.github.seqware.queryengine.model.Analysis: Constant prefix="Analysis"
prefix - Static variable in interface com.github.seqware.queryengine.model.AnalysisSet: Constant prefix="AnalysisSet"
prefix - Static variable in class com.github.seqware.queryengine.model.FeatureSet: Constant prefix="FeatureSet"
prefix - Static variable in interface com.github.seqware.queryengine.model.Group: Constant prefix="Group"
prefix - Static variable in class com.github.seqware.queryengine.model.impl.FeatureList: Constant prefix="Feature"
prefix - Static variable in interface com.github.seqware.queryengine.model.Reference: Constant prefix="Reference"
prefix - Static variable in interface com.github.seqware.queryengine.model.ReferenceSet: Constant prefix="ReferenceSet"
prefix - Static variable in class com.github.seqware.queryengine.model.Tag: Constant prefix="Tag"
prefix - Static variable in interface com.github.seqware.queryengine.model.TagSet: Constant prefix="TagSet"
prefix - Static variable in class com.github.seqware.queryengine.model.User: Constant prefix="User"
prepareData(WorkflowInfo, String, ArrayList<String>, Map<String, String>, boolean, ArrayList<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow: prepareData.
prependToFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
PrepQCgenomes - Class in net.sourceforge.seqware.pipeline.modules.qc: Prepare the "QC Genomes" database from external sources.
PrepQCgenomes() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.PrepQCgenomes
PrepTranscriptDB - Class in net.sourceforge.seqware.pipeline.modules.alignment: Given a set of database tables, construct a reference set of transcripts.
PrepTranscriptDB() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.PrepTranscriptDB
prettyPrint(String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools: prettyPrint.
print(Writer, ReturnValue, String, boolean, FileMetadata) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Prints a line to the Excel spreadsheet.
print(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: print.
print(String) - Method in class net.sourceforge.seqware.pipeline.plugins.Metadata: print.
printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: printAndAppendtoStderr.
printAndAppendtoStderr(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner: printAndAppendtoStderr.
printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: printAndAppendtoStdout.
printAndAppendtoStdout(String) - Method in class net.sourceforge.seqware.pipeline.runner.Runner: printAndAppendtoStdout.
printAndAppendtoString(String, String) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr: printAndAppendtoString.
printHeader(Writer, boolean) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Print the header of the Excel spreadsheet to file.
println(String) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: println.
printTSVFile(Writer, boolean, List<ReturnValue>, String) - Static method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: printTSVFile.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor: process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor: process.
process(Object) - Method in interface net.sourceforge.seqware.queryengine.tools.iterators.processors.ProcessorInterface: process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: process.
process(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor: process.
processArgs(Option, ListIterator) - Method in class org.apache.commons.cli.HackedPosixParser
processExitStatus - Variable in class net.sourceforge.seqware.common.module.ReturnValue
ProcessIdProcessResource - Class in net.sourceforge.seqware.webservice.resources.queries: ProcessIdProcessResource class.
ProcessIdProcessResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.ProcessIdProcessResource: Constructor for ProcessIdProcessResource.
ProcessIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: ProcessIDResource class.
ProcessIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource: Constructor for ProcessIDResource.
Processing - Class in net.sourceforge.seqware.common.model
Processing() - Constructor for class net.sourceforge.seqware.common.model.Processing: Constructor for Processing.
PROCESSING - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant PROCESSING=100
processing - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
PROCESSING_ALGO - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PROCESSING_ALGO="Header.PROCESSING_ALGO.getTitle()"
PROCESSING_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PROCESSING_ATTRIBUTES="Header.PROCESSING_ATTRIBUTES.getTitle()"
PROCESSING_DATE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PROCESSING_DATE="Header.PROCESSING_DATE.getTitle()"
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: processing_event_to_task_group.
processing_event_to_task_group(int, int[], int[], String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: processing_event_to_task_group.
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: processing_event_to_task_group.
processing_event_to_task_group(int, int[], int[], String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: processing_event_to_task_group.
PROCESSING_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant PROCESSING_PREFIX="ae_"
PROCESSING_SWID - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PROCESSING_SWID="Header.PROCESSING_SWID.getTitle()"
PROCESSING_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant PROCESSING_TAG_PREFIX="Header.PROCESSING_TAG_PREFIX.getTitle()"
processingAccession - Variable in class net.sourceforge.seqware.pipeline.module.Module
ProcessingAttribute - Class in net.sourceforge.seqware.common.model: ProcessingAttribute generated by hbm2java
ProcessingAttribute() - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute: Constructor for ProcessingAttribute.
ProcessingAttribute(int, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute: Constructor for ProcessingAttribute.
ProcessingAttribute(int, Processing, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingAttribute: Constructor for ProcessingAttribute.
ProcessingAttributeDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingAttributeDAO interface.
ProcessingAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingAttributeDAOHibernate class.
ProcessingAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate
ProcessingController - Class in net.sourceforge.solexatools.webapp.controller: SequencerRunController
ProcessingController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController: Constructor for ProcessingController.
ProcessingController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingController: Constructor for ProcessingController.
ProcessingDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingDAO interface.
ProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingDAOHibernate class.
ProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: Constructor for ProcessingDAOHibernate.
ProcessingDataStructure2Dot - Class in net.sourceforge.seqware.pipeline.plugins
ProcessingDataStructure2Dot() - Constructor for class net.sourceforge.seqware.pipeline.plugins.ProcessingDataStructure2Dot
ProcessingExperiments - Class in net.sourceforge.seqware.common.model: ProcessingExperiments generated by hbm2java
ProcessingExperiments() - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments: Constructor for ProcessingExperiments.
ProcessingExperiments(int, Processing, Experiment) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments: Constructor for ProcessingExperiments.
ProcessingExperiments(int, Processing, Experiment, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingExperiments: Constructor for ProcessingExperiments.
ProcessingExperimentsDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingExperimentsDAO interface.
ProcessingExperimentsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingExperimentsDAOHibernate class.
ProcessingExperimentsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate
ProcessingExperimentsService - Interface in net.sourceforge.seqware.common.business: ProcessingExperimentsService interface.
ProcessingExperimentsServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingExperimentsServiceImpl class.
ProcessingExperimentsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl
ProcessingIus - Class in net.sourceforge.seqware.common.model: ProcessingIus generated by hbm2java
ProcessingIus() - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus: Constructor for ProcessingIus.
ProcessingIus(int, IUS, Processing) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus: Constructor for ProcessingIus.
ProcessingIus(int, IUS, Processing, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingIus: Constructor for ProcessingIus.
ProcessingIUSDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingIUSDAO interface.
ProcessingIUSDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingIUSDAOHibernate class.
ProcessingIUSDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate
ProcessingIUSService - Interface in net.sourceforge.seqware.common.business: ProcessingIUSService interface.
ProcessingIUSServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingIUSServiceImpl class.
ProcessingIUSServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl
ProcessingLanes - Class in net.sourceforge.seqware.common.model: ProcessingLanes generated by hbm2java
ProcessingLanes() - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes: Constructor for ProcessingLanes.
ProcessingLanes(int, Processing, Lane) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes: Constructor for ProcessingLanes.
ProcessingLanes(int, Processing, Lane, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingLanes: Constructor for ProcessingLanes.
ProcessingLanesDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingLanesDAO interface.
ProcessingLanesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingLanesDAOHibernate class.
ProcessingLanesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate
ProcessingLanesService - Interface in net.sourceforge.seqware.common.business: ProcessingLanesService interface.
ProcessingLanesServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingLanesServiceImpl class.
ProcessingLanesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl
ProcessingList - Class in net.sourceforge.seqware.common.model.lists: ProcessingList class.
ProcessingList() - Constructor for class net.sourceforge.seqware.common.model.lists.ProcessingList: Constructor for ProcessingList.
ProcessingRelationship - Class in net.sourceforge.seqware.common.model: ProcessingRelationship generated by hbm2java
ProcessingRelationship() - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship: Constructor for ProcessingRelationship.
ProcessingRelationship(int) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship: Constructor for ProcessingRelationship.
ProcessingRelationship(int, Processing, Processing, String) - Constructor for class net.sourceforge.seqware.common.model.ProcessingRelationship: Constructor for ProcessingRelationship.
ProcessingRelationshipDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingRelationshipDAO interface.
ProcessingRelationshipDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingRelationshipDAOHibernate class.
ProcessingRelationshipDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate
ProcessingRelationshipService - Interface in net.sourceforge.seqware.common.business: ProcessingRelationshipService interface.
ProcessingRelationshipServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingRelationshipServiceImpl class.
ProcessingRelationshipServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl
ProcessingResource - Class in net.sourceforge.seqware.queryengine.webservice.view: ProcessingResource class.
ProcessingResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.ProcessingResource
ProcessingSamples - Class in net.sourceforge.seqware.common.model: ProcessingSamples generated by hbm2java
ProcessingSamples() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples: Constructor for ProcessingSamples.
ProcessingSamples(int, Processing, Sample) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples: Constructor for ProcessingSamples.
ProcessingSamples(int, Processing, Sample, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSamples: Constructor for ProcessingSamples.
ProcessingSamplesDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingSamplesDAO interface.
ProcessingSamplesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingSamplesDAOHibernate class.
ProcessingSamplesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate
ProcessingSamplesService - Interface in net.sourceforge.seqware.common.business: ProcessingSamplesService interface.
ProcessingSamplesServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingSamplesServiceImpl class.
ProcessingSamplesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl
processingsCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils: Returns count of the Sample related Workflow Runs.
ProcessingSequencerRuns - Class in net.sourceforge.seqware.common.model: ProcessingSequencerRuns generated by hbm2java
ProcessingSequencerRuns() - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Constructor for ProcessingSequencerRuns.
ProcessingSequencerRuns(int, Processing, SequencerRun) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Constructor for ProcessingSequencerRuns.
ProcessingSequencerRuns(int, Processing, SequencerRun, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Constructor for ProcessingSequencerRuns.
ProcessingSequencerRunsDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingSequencerRunsDAO interface.
ProcessingSequencerRunsDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingSequencerRunsDAOHibernate class.
ProcessingSequencerRunsDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate
ProcessingSequencerRunsService - Interface in net.sourceforge.seqware.common.business: ProcessingSequencerRunsService interface.
ProcessingSequencerRunsServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingSequencerRunsServiceImpl class.
ProcessingSequencerRunsServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl
ProcessingService - Interface in net.sourceforge.seqware.common.business: ProcessingService interface.
ProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingServiceImpl class.
ProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: Constructor for ProcessingServiceImpl.
ProcessingSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
ProcessingSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController: Constructor for ProcessingSetupController.
ProcessingStudies - Class in net.sourceforge.seqware.common.model: ProcessingStudies generated by hbm2java
ProcessingStudies() - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies: Constructor for ProcessingStudies.
ProcessingStudies(int, Processing, Study) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies: Constructor for ProcessingStudies.
ProcessingStudies(int, Processing, Study, String, String, String, Integer) - Constructor for class net.sourceforge.seqware.common.model.ProcessingStudies: Constructor for ProcessingStudies.
ProcessingStudiesDAO - Interface in net.sourceforge.seqware.common.dao: ProcessingStudiesDAO interface.
ProcessingStudiesDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProcessingStudiesDAOHibernate class.
ProcessingStudiesDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate
ProcessingStudiesService - Interface in net.sourceforge.seqware.common.business: ProcessingStudiesService interface.
ProcessingStudiesServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProcessingStudiesServiceImpl class.
ProcessingStudiesServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl
ProcessingTaskGroup - Class in net.sourceforge.seqware.common.metadata.ProcessingTaskGroup: Standalone application to insert a new processing task group into the database.
ProcessingTaskGroup() - Constructor for class net.sourceforge.seqware.common.metadata.ProcessingTaskGroup.ProcessingTaskGroup
ProcessorInterface - Interface in net.sourceforge.seqware.queryengine.tools.iterators.processors: ProcessorInterface interface.
ProcessResource - Class in net.sourceforge.seqware.webservice.resources.tables: ProcessResource class.
ProcessResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.ProcessResource: Constructor for ProcessResource.
processTemplate(String[], String, String, Map<String, String>, String[]) - Method in class net.sourceforge.seqware.pipeline.daxgenerator.Daxgenerator: processTemplate.
ProcessTools - Class in net.sourceforge.seqware.common.util.processtools: Sleep for N seconds.
ProcessTools() - Constructor for class net.sourceforge.seqware.common.util.processtools.ProcessTools
processVCFTagSpec(String, TagSet, CreateUpdateManager) - Static method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker: processVCFTagSpec.
PROGRAMFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant PROGRAMFAILED=1
Project - Class in net.sourceforge.seqware.common.model: Project class.
Project() - Constructor for class net.sourceforge.seqware.common.model.Project: Constructor for Project.
ProjectDAO - Interface in net.sourceforge.seqware.common.dao: ProjectDAO interface.
ProjectDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ProjectDAOHibernate class.
ProjectDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: Constructor for ProjectDAOHibernate.
projectid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
ProjectService - Interface in net.sourceforge.seqware.common.business: ProjectService interface.
ProjectServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ProjectServiceImpl class.
ProjectServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: Constructor for ProjectServiceImpl.
PropagateOwnership - Class in net.sourceforge.seqware.common.hibernate: Should only be used for one query and then discarded and re-instantiated.
PropagateOwnership() - Constructor for class net.sourceforge.seqware.common.hibernate.PropagateOwnership: Constructor for PropagateOwnership.
protect - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
ProtobufSerialization - Class in com.github.seqware.queryengine.impl: ProtobufSerialization class.
ProtobufSerialization() - Constructor for class com.github.seqware.queryengine.impl.ProtobufSerialization
ProtobufTransferInterface<S extends com.google.protobuf.Message,T extends Atom> - Interface in com.github.seqware.queryengine.impl.protobufIO: Interface for conversion from protein buffer auto-generated objects to model and vice versa
ProvisionDependenciesBundle - Class in net.sourceforge.seqware.pipeline.modules.utilities: Purpose: This module takes a software bundle and unzips it to the temporary directory.
ProvisionDependenciesBundle() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
provisionFile(String, String) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.BulkProvisionFiles: This method was tested with: # local to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file /tmp/foo --output-dir /tmp/tmp2 # local to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file /tmp/foo --output-dir s3://seqware.bundles/dependencies/data # http to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file https://s3.amazonaws.com/seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir /tmp/tmp2 # http to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file https://s3.amazonaws.com/seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir s3://seqware.bundles/dependencies/noarch # S3 to local ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file s3://seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir /tmp/tmp2 # S3 to S3 ./bin/seqware-runner.sh --no-metadata --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles -- --input-file s3://seqware.bundles/dependencies/data/AboutStacks.pdf.zip --output-dir s3://seqware.bundles/dependencies/noarch
provisionFile(String, String, boolean, ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: provisionFile.
ProvisionFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities: Purpose: This module takes one or more inputs (S3 URL, HTTP/HTTPS URL, or local file path) and copies the file to the specified output (S3 bucket URL, HTTP/HTTPS URL, or local directory path).
ProvisionFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
ProvisionFilesJob - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
ProvisionFilesJob(AbstractJob, String, SqwFile, String) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
ProvisionFilesUtil - Class in net.sourceforge.seqware.common.util.filetools: ProvisionFilesUtil class.
ProvisionFilesUtil() - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Default ctor.
ProvisionFilesUtil(boolean) - Constructor for class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Set verbose mode ctor.
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.DatabaseIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ExperimentIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.IusIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.LaneIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.ProcessIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource
put(Representation) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource
put(HttpServletRequest) - Static method in class net.sourceforge.solexatools.Debug: put.
put(String) - Static method in class net.sourceforge.solexatools.Debug: put.
put(Object, String) - Static method in class net.sourceforge.solexatools.Debug: put.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putConsequence.
putConsequence(Consequence, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putConsequence.
putConsequence(Consequence) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putConsequence.
putConsequence(Consequence, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putConsequence.
putConsequence(Consequence) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putConsequence.
putCoverage(Integer, Integer) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putCoverage.
putCoverage(Coverage) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putCoverage.
putCoverage(Coverage, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putCoverage.
putCoverage(Coverage) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putCoverage.
putCoverage(Coverage, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putCoverage.
putDestination(BufferedInputStream, String, int, String, ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles: HTTP writeback currently not supported S3 uses multi-part upload which should deal with failed uploads (maybe) I'm not really dealing with failed upload recovery here...
putFeature(FeatureSet, Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putFeature.
putFeature(Feature) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putFeature.
putFeature(Feature, SeqWareIterator, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putFeature.
putFeature(Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putFeature.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putMismatch.
putMismatch(Variant) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: putMismatch.
putMismatch(Variant) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putMismatch.
putMismatch(Variant, SeqWareIterator, boolean) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: putMismatch.
putModel(Database, TupleBinding, Model, Long, SeqWareIterator, boolean) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: putModel.
putModel(String, LocatableModel, TupleBinding, HTable, HTable, HTable, String, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: FIXME: what happens if something steps on this load below and creates a timestamp that exists already? may need to look at transaction support or making this syncronized (won't matter if other client on other machine overwrites this timestamp!)
putModel(String, String, String, TupleBinding, LocatableModel) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: putModel.
putTag(Tag, Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: putTag.
putToHttp() - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Not supported yet.
putToS3(BufferedInputStream, String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Copy file using reader into output.
putToS3(InputStream, String, Cipher, Cipher) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Copy file using reader into output.

Q

QCGenome - Class in net.sourceforge.seqware.pipeline.modules.qc: To get alignment to QC genome, currenly, human rRNA and viral genome Underlying script: sw_module_RiboAndViralAln.pl (by Sara Grimm) Necessary programs: perl path to BWA Expected output: "mock" alignment to qc genome, text file with key values
QCGenome() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.QCGenome
qcreport - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
QEMapper<KEYOUT,VALUEOUT> - Class in com.github.seqware.queryengine.plugins.hbasemr: Base mapper class used by all Query Engine plug-ins.
QEMapper() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
QEReducer<KEYIN,VALUEIN,KEYOUT,VALUEOUT> - Class in com.github.seqware.queryengine.plugins.hbasemr: Base reducer class used by all plug-ins.
QEReducer() - Constructor for class com.github.seqware.queryengine.plugins.hbasemr.QEReducer
QESupporting - Class in com.github.seqware.queryengine.dto
QESupporting.AtomPB - Class in com.github.seqware.queryengine.dto
QESupporting.AtomPB.Builder - Class in com.github.seqware.queryengine.dto
QESupporting.AtomPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QESupporting.FeatureAtomPB - Class in com.github.seqware.queryengine.dto
QESupporting.FeatureAtomPB.Builder - Class in com.github.seqware.queryengine.dto
QESupporting.FeatureAtomPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QESupporting.FSGIDPB - Class in com.github.seqware.queryengine.dto
QESupporting.FSGIDPB.Builder - Class in com.github.seqware.queryengine.dto
QESupporting.FSGIDPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QESupporting.SGIDPB - Class in com.github.seqware.queryengine.dto
QESupporting.SGIDPB.Builder - Class in com.github.seqware.queryengine.dto
QESupporting.SGIDPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QESupporting.TagPB - Class in com.github.seqware.queryengine.dto
QESupporting.TagPB.Builder - Class in com.github.seqware.queryengine.dto
QESupporting.TagPBOrBuilder - Interface in com.github.seqware.queryengine.dto
qtype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
qualFilter - Class in net.sourceforge.seqware.pipeline.modules.qc: Performing quality flitering on sequence read Underlying script: sw_module_qualFilter.pl (by Sara Grimm as base_quality_scan.pl) Necessary programs: perl Expected output: qual_filter.txt
qualFilter() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.qualFilter
qualityscorer - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES
qualityscores - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING
qualStat - Class in net.sourceforge.seqware.pipeline.modules.qc: Performing per lane based statistics Underlying script: fastx_quality_stats executable installed Dependency: fastx_quality_stats from http://hannonlab.cshl.edu/fastx_toolkit/commandline.html Currently installed at: /usr/bin/fastx_quality_stats Expected output: qual_filter.txt
qualStat() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.qualStat
query() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: query.
QUERY_PARAM_FILE - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper: Constant QUERY_PARAM_FILE='p'
QUERY_PARAM_STRING - Static variable in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper: Constant QUERY_PARAM_STRING='s'
QueryDumperInterface - Interface in com.github.seqware.queryengine.system.exporters: This interface should be extended by a class that a developer wishes to use as input to the QueryVCFDumper.
QueryEngine - Class in com.github.seqware.queryengine.dto
QueryEngine.ACLPB - Class in com.github.seqware.queryengine.dto
QueryEngine.ACLPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.ACLPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.AnalysisPB - Class in com.github.seqware.queryengine.dto
QueryEngine.AnalysisPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.AnalysisPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.AnalysisSetPB - Class in com.github.seqware.queryengine.dto
QueryEngine.AnalysisSetPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.AnalysisSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.FeatureListPB - Class in com.github.seqware.queryengine.dto
QueryEngine.FeatureListPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.FeatureListPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.FeaturePB - Class in com.github.seqware.queryengine.dto
QueryEngine.FeaturePB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.FeaturePB.StrandPB - Enum in com.github.seqware.queryengine.dto
QueryEngine.FeaturePBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.FeatureSetPB - Class in com.github.seqware.queryengine.dto
QueryEngine.FeatureSetPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.FeatureSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.GroupPB - Class in com.github.seqware.queryengine.dto
QueryEngine.GroupPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.GroupPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.MoleculePB - Class in com.github.seqware.queryengine.dto
QueryEngine.MoleculePB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.MoleculePBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.ReferencePB - Class in com.github.seqware.queryengine.dto
QueryEngine.ReferencePB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.ReferencePBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.ReferenceSetPB - Class in com.github.seqware.queryengine.dto
QueryEngine.ReferenceSetPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.ReferenceSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.TagSetPB - Class in com.github.seqware.queryengine.dto
QueryEngine.TagSetPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.TagSetPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryEngine.UserPB - Class in com.github.seqware.queryengine.dto
QueryEngine.UserPB.Builder - Class in com.github.seqware.queryengine.dto
QueryEngine.UserPBOrBuilder - Interface in com.github.seqware.queryengine.dto
QueryFuture<ReturnType> - Interface in com.github.seqware.queryengine.model: This interface sketches out the result that might be returned from a asynchronous query.
QueryInterface - Interface in com.github.seqware.queryengine.model: This interface allows users to access queries that are built into the query engine, as well as install/un-install plug-ins that allow the user to perform additional annotation and/or other operations (in other words, this handles the R operations from CRUD)).
QueryInterface.Location - Enum in com.github.seqware.queryengine.model: Type of location query.
queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
queryValues - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
QueryVCFDumper - Class in com.github.seqware.queryengine.system.exporters: Exporter using a new interface to the parameters in order to support queries triggerable from the command-line.
QueryVCFDumper() - Constructor for class com.github.seqware.queryengine.system.exporters.QueryVCFDumper
QUEUED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant QUEUED=101

R

r - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
random - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
RandomInvitationCode - Class in net.sourceforge.seqware.common.invitation: RandomInvitationCode class.
RandomInvitationCode() - Constructor for class net.sourceforge.seqware.common.invitation.RandomInvitationCode: Constructor for RandomInvitationCode.
RandomInvitationCode - Class in net.sourceforge.solexatools.util: RandomInvitationCode class.
RandomInvitationCode() - Constructor for class net.sourceforge.solexatools.util.RandomInvitationCode: Constructor for RandomInvitationCode.
read(Kryo, Input) - Method in class com.github.seqware.queryengine.util.FSGID
read(Kryo, Input) - Method in class com.github.seqware.queryengine.util.SGID
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
READ_ATTEMPTS - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
readBases - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
readclass - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
readCount - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
readindex - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
readspec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC
readsSupportingCallOne - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
readsSupportingCallThree - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
readsSupportingCallTwo - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
readTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: readTags.
readTags(Model, String) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: readTags.
readtype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC
rebuild() - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet: Rebuild the underlying set architecture.
rebuild() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Rebuild the underlying set architecture.
rebuild() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Rebuild the underlying set architecture.
rebuild() - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface: Rebuild the underlying set architecture.
redirect() - Method in class net.sourceforge.seqware.pipeline.runner.DefaultConfig: redirect.
REDIRECT - Static variable in interface net.sourceforge.seqware.pipeline.runner.RunnerParams.Bean
RedirectAspect - Class in net.sourceforge.seqware.pipeline.runner: We need to clarify that there are two issues here.
RedirectAspect() - Constructor for class net.sourceforge.seqware.pipeline.runner.RedirectAspect
RedirectAware - Interface in net.sourceforge.seqware.pipeline.module: This module, in conjunction with the Tag and Run annotation are used to replace the old Module with the Runner code.
reduce(FeatureSet, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: Reduce implementation that takes mapped atoms and processes them.
reduce(FeatureSet, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin: Reduce implementation that takes mapped atoms and processes them.
reduce(FeatureSet, FeatureSet) - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin: Reduce implementation that takes mapped atoms and processes them.
reduce(S, S) - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin: Reduce implementation that takes mapped atoms and processes them.
reduceInit() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: reduceInit.
reduceInit() - Method in class com.github.seqware.queryengine.plugins.inmemory.InMemoryFeaturesByFilterPlugin: reduceInit.
reduceInit() - Method in class com.github.seqware.queryengine.plugins.lazyinmemory.LazyFeaturesByAttributesPlugin: reduceInit.
reduceInit() - Method in interface com.github.seqware.queryengine.plugins.MapReducePlugin: reduceInit.
Reference - Interface in com.github.seqware.queryengine.model: A reference is a particular build version such as "hg19" or "hg18".
reference - Variable in class com.github.seqware.queryengine.model.Reference.Builder
Reference.Builder - Class in com.github.seqware.queryengine.model
Reference.Builder() - Constructor for class com.github.seqware.queryengine.model.Reference.Builder
REFERENCE_ID_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant REFERENCE_ID_PARAM='r'
referencealignment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
referenceAveSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
referenceBase - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
referenceCache - Variable in class com.github.seqware.queryengine.util.LazyReference
referenceCallQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
referenceChecked - Variable in class com.github.seqware.queryengine.util.LazyReference
ReferenceCreator - Class in com.github.seqware.queryengine.system: Quick and dirty ReferenceCreator.
ReferenceCreator() - Constructor for class com.github.seqware.queryengine.system.ReferenceCreator: Constructor for ReferenceCreator.
referenceId - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
REFERENCEID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
REFERENCEIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
ReferenceIO - Class in com.github.seqware.queryengine.impl.protobufIO: ReferenceIO class.
ReferenceIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.ReferenceIO
referenceMaxSeqQuality - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
ReferenceSet - Interface in com.github.seqware.queryengine.model: A ReferenceSet is a collection of references which are a collection of contigs and coordinates.
ReferenceSet.Builder - Class in com.github.seqware.queryengine.model
ReferenceSet.Builder() - Constructor for class com.github.seqware.queryengine.model.ReferenceSet.Builder
ReferenceSetIO - Class in com.github.seqware.queryengine.impl.protobufIO: ReferenceSetIO class.
ReferenceSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.ReferenceSetIO
referenceSGID - Variable in class com.github.seqware.queryengine.util.LazyReference
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF
refname - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
REFNAME_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
refRegex - Static variable in class com.github.seqware.queryengine.Constants: Regular Expression for suitable rowKeys
refresh(Atom) - Method in interface com.github.seqware.queryengine.impl.BackEndInterface: Update the obj using the latest information from the back-end
refresh(Atom) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Update the obj using the latest information from the back-end
region - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
registerAllExtensions(ExtensionRegistry) - Static method in class com.github.seqware.queryengine.dto.QESupporting
registerAllExtensions(ExtensionRegistry) - Static method in class com.github.seqware.queryengine.dto.QueryEngine
Registration - Class in net.sourceforge.seqware.common.model: Registration
Registration() - Constructor for class net.sourceforge.seqware.common.model.Registration: Constructor for Registration.
registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicResource
registration - Variable in class net.sourceforge.seqware.webservice.resources.BasicRestlet
RegistrationController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationController class.
RegistrationController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController: Constructor for RegistrationController.
RegistrationController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationController: Constructor for RegistrationController.
RegistrationDAO - Interface in net.sourceforge.seqware.common.dao: RegistrationDAO interface.
RegistrationDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: RegistrationDAOHibernate class.
RegistrationDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate: Constructor for RegistrationDAOHibernate.
RegistrationDTO - Class in net.sourceforge.seqware.common.model
RegistrationDTO() - Constructor for class net.sourceforge.seqware.common.model.RegistrationDTO: Constructor for RegistrationDTO.
RegistrationService - Interface in net.sourceforge.seqware.common.business: RegistrationService interface.
RegistrationServiceImpl - Class in net.sourceforge.seqware.common.business.impl: RegistrationServiceImpl class.
RegistrationServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: Constructor for RegistrationServiceImpl.
RegistrationSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
RegistrationSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController: Constructor for RegistrationSetupController.
RegistrationValidator - Class in net.sourceforge.solexatools.validation: RegistrationValidator class.
RegistrationValidator() - Constructor for class net.sourceforge.solexatools.validation.RegistrationValidator: Constructor for RegistrationValidator.
relativeLocation - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
release - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
releaseLock() - Method in class com.github.seqware.queryengine.system.importers.Importer: releaseLock.
releaseLock() - Method in class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock: Deprecated. releaseLock.
releaseLock() - Method in class net.sourceforge.seqware.queryengine.tools.importers.Importer: releaseLock.
releaseStore(String) - Static method in class net.sourceforge.seqware.queryengine.webservice.model.BackendPool: releaseStore.
remove() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.FeatureScanIterator
remove() - Method in class com.github.seqware.queryengine.impl.HBaseStorage.ScanIterator
remove(Feature) - Method in class com.github.seqware.queryengine.model.FeatureSet: Remove one element
remove() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl.TagValueIterator
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.FeatureList: remove.
remove(T) - Method in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet: Remove one element
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Remove one element
remove() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.BatchedRowFeatureListsIterator
remove() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.ConsolidatedFeatureIterator
remove(Feature) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Remove one element
remove(T) - Method in interface com.github.seqware.queryengine.model.interfaces.MolSetInterface: Remove one element
remove() - Method in class com.github.seqware.queryengine.util.SeqWareIterator: Removal of subjects cannot be done implicitly from an iterator -- this method is not supported.
remove() - Method in class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.CursorIterator: remove.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseModelIterator: Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.HBaseTagModelIterator: Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresModelIterator: Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresTagModelIterator: Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.PostgresVariantModelIterator: Removes are unimplemented.
remove() - Method in class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: remove.
removeAnalysisIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
removeFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
removeFeatures(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
removeFeatureSetIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
removeGrps(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
RemoveIndelsAndTrim - Class in net.sourceforge.seqware.pipeline.modules.BamFilters: Purpose: Module to wrap remove_indels_and_trim script.
RemoveIndelsAndTrim() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveIndelsAndTrim
removeReferenceIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
removeSelectedItemsCurrentParam(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: removeSelectedItemsCurrentParam.
removeSelectedItemsLaunchWorkflow(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: removeSelectedItemsLaunchWorkflow.
removeSequencerRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: removeSequencerRun.
RemoveSingleIndelNotOnEnds - Class in net.sourceforge.seqware.pipeline.modules.BamFilters: Purpose: Module to wrap remove_indels_and_trim script.
RemoveSingleIndelNotOnEnds() - Constructor for class net.sourceforge.seqware.pipeline.modules.BamFilters.RemoveSingleIndelNotOnEnds
removeStudy(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: removeStudy.
removeTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
removeTags(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
removeTagSpecIDs(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
removeUsers(int) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
removeWorkflowRun(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: removeWorkflowRun.
removeWorkflowRunRunning(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: removeWorkflowRunRunning.
replace(String, String) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils: resolve all the FTL variables ${variable} in the string with the variables in maps
replace(String, Map<String, String>) - Static method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils: replace.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: report.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageStatsProcessor: report.
report() - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.MismatchConsequenceReportProcessor: report.
report(Object) - Method in interface net.sourceforge.seqware.queryengine.tools.iterators.processors.ProcessorInterface: report.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: report.
report(Object) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor: report.
reportCardSingle - Class in net.sourceforge.seqware.pipeline.modules.quantification: Generating report card on RNAseq against Microarray - Agilent 244k array.
reportCardSingle() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.reportCardSingle
reportError(RecognitionException) - Method in class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageLexerWrapper
reportError(RecognitionException) - Method in class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageParserWrapper
reportException(ImportWorker) - Method in class com.github.seqware.queryengine.system.importers.FeatureImporter: reportException.
ReportTest - Class in net.sourceforge.seqware.pipeline.tools: ReportTest class.
ReportTest() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest
ReportTest.TestThread - Class in net.sourceforge.seqware.pipeline.tools
ReportTest.TestThread() - Constructor for class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CachedTagResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.ConsequenceResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CoverageResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.CoveragesResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.FileResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GeneReportResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.LiveTagResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.MismatchesResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.MismatchResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.ProcessingResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.TagResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.TemplateResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.VersionResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource: represent.
represent() - Method in class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource: represent.
Requirement - Class in net.sourceforge.seqware.pipeline.workflowV2.model
Requirement() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
Requirement.Type - Enum in net.sourceforge.seqware.pipeline.workflowV2.model: enum of all Type
requireRegistration(HttpServletRequest, HttpServletResponse) - Static method in class net.sourceforge.solexatools.Security: requireRegistration.
rerunWorkflowRun(List<String>, List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider: Returns true only if there are more files to run than have been run on any workflow so far, or if the filesToRun have different filepaths than those that have been run before.
resetCompletedChildren() - Method in class net.sourceforge.seqware.common.model.Processing: resetCompletedChildren.
resetRunningChildren() - Method in class net.sourceforge.seqware.common.model.Processing: resetRunningChildren.
RESUBMITTED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant RESUBMITTED="resubmitted"
ret - Variable in class net.sourceforge.seqware.pipeline.bundle.Bundle
ret - Variable in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
ret - Variable in class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
ret - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
RETURNEDHELPMSG - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant RETURNEDHELPMSG=110
ReturnValue - Class in net.sourceforge.seqware.common.module: Return values > 0 are errors that will cause the runner to exit.
ReturnValue() - Constructor for class net.sourceforge.seqware.common.module.ReturnValue: Constructor for ReturnValue.
ReturnValue(int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue: Constructor for ReturnValue.
ReturnValue(String, String, int) - Constructor for class net.sourceforge.seqware.common.module.ReturnValue: Constructor for ReturnValue.
returnValue - Variable in class net.sourceforge.seqware.common.module.ReturnValue
ReturnValue.ExitStatus - Enum in net.sourceforge.seqware.common.module
ReturnValueList - Class in net.sourceforge.seqware.common.model.lists: ReturnValueList class.
ReturnValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.ReturnValueList: Constructor for ReturnValueList.
RIGHTS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
root - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
RootSampleResource - Class in net.sourceforge.seqware.webservice.resources.tables: This resource should pull back only samples without parents
RootSampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.RootSampleResource: Constructor for RootSampleResource.
ROWKEY_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant ROWS_PER_PAGE="rp"
ROWS_PER_PAGE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant ROWS_PER_PAGE="rp"
RPNStack - Class in com.github.seqware.queryengine.kernel: A stack of arguments and operations in Reverse Polish Notation (RPN, http://en.wikipedia.org/wiki/Reverse_Polish_notation).
RPNStack(Object...) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack: Constructor for RPNStack.
RPNStack(List) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack: Constructor for RPNStack.
RPNStack.Constant - Class in com.github.seqware.queryengine.kernel
RPNStack.Constant(Object) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.Constant
RPNStack.FeatureAttribute - Class in com.github.seqware.queryengine.kernel: Represents attributes of features that are passed as parameter.
RPNStack.FeatureAttribute(String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.FeatureAttribute
RPNStack.Operation - Enum in com.github.seqware.queryengine.kernel: Operations for combining query constraints.
RPNStack.Parameter - Class in com.github.seqware.queryengine.kernel
RPNStack.Parameter(String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.Parameter
RPNStack.TagHierarchicalOccurrence - Class in com.github.seqware.queryengine.kernel: Represents tags whose occurrence is tested -- including the tags children!
RPNStack.TagHierarchicalOccurrence(String, String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagHierarchicalOccurrence
RPNStack.TagOccurrence - Class in com.github.seqware.queryengine.kernel: Represents tags whose occurrence is probed.
RPNStack.TagOccurrence(String, String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagOccurrence
RPNStack.TagValue - Class in com.github.seqware.queryengine.kernel: Represents tags whose value is retrieved
RPNStack.TagValue(String, String) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagValue
RPNStack.TagValuePresence - Class in com.github.seqware.queryengine.kernel: Represents tag/value pairs that should be present.
RPNStack.TagValuePresence(String, String, Tag.ValueType, Object) - Constructor for class com.github.seqware.queryengine.kernel.RPNStack.TagValuePresence
run() - Method in class com.github.seqware.queryengine.system.importers.workers.GFF3VariantImportWorker
run() - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
run() - Method in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker
run() - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread
run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.PluginRunner: run.
run(String[]) - Method in class net.sourceforge.seqware.pipeline.runner.Runner: run.
run() - Method in class net.sourceforge.seqware.pipeline.runner.Runner2: run.
run() - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.BedFeatureImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.GFF3VariantImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.PileupVariantImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.U87LargeDeletionVariantImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.U87TranslocationVariantImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.VCFVariantImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.VenterGenomeVariantImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.WatsonGenomeVariantImportWorker: run.
run() - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.YanHuangGenomeVariantImportWorker: run.
run - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunSet
runattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
runattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
runCenter - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
runCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: runCommand.
runCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: runCommand.
runCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: runCommand.
runCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: A simple command runner that captures the return value of the program.
runDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
runFile - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
runInSessionCalculations() - Method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions: runInSessionCalculations.
runlink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
runlinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
runMain(String[]) - Static method in class com.github.seqware.queryengine.system.exporters.QueryVCFDumper: Interface for mock-testing
runMain(String[]) - Static method in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Interface for mock-testing
Runner - Class in net.sourceforge.seqware.pipeline.runner: Runner class.
Runner() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner
Runner.Keys - Interface in net.sourceforge.seqware.pipeline.runner
Runner2 - Class in net.sourceforge.seqware.pipeline.runner: This is a new Runner class that is designed (hopefuly) to replace the current Runner class.
Runner2() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner2
Runner2.ModuleConfig - Class in net.sourceforge.seqware.pipeline.runner: This class is used to configure the instantiating of a module
Runner2.ModuleConfig() - Constructor for class net.sourceforge.seqware.pipeline.runner.Runner2.ModuleConfig
RUNNERERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant RUNNERERR=91
RunnerParams - Class in net.sourceforge.seqware.pipeline.runner: This class is used to pass information from the Runner class to the Configuration class, which can instantiate the module and setup the bean.
RunnerParams() - Constructor for class net.sourceforge.seqware.pipeline.runner.RunnerParams: Constructor for RunnerParams.
RunnerParams.Bean - Interface in net.sourceforge.seqware.pipeline.runner
RUNNING - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant RUNNING="running"
RUNNING - Static variable in class net.sourceforge.seqware.common.model.WorkflowRun: Constant RUNNING="running"
RUNNING - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider: Constant RUNNING="running"
RUNNING - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin: Constant RUNNING="running"
runref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
RunSet - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunSet
runStartTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue
runStopTstmp - Variable in class net.sourceforge.seqware.common.module.ReturnValue
RUNTIMEEXCEPTION - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant RUNTIMEEXCEPTION=6
RunTools - Class in net.sourceforge.seqware.common.util.runtools: RunTools class.
RunTools() - Constructor for class net.sourceforge.seqware.common.util.runtools.RunTools
RunType - Class in net.sourceforge.seqware.queryengine.webservice.model: A Run contains the sequencing results from a particular run on a sequencing instrument.
RunType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType
RunType.DATABLOCK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.DATABLOCK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
RunType.DATABLOCK.FILES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.DATABLOCK.FILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES
RunType.DATABLOCK.FILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.DATABLOCK.FILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE
RunType.EXPERIMENTREF - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.EXPERIMENTREF() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF
RunType.RUNATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.RUNATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES
RunType.RUNATTRIBUTES.RUNATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.RUNATTRIBUTES.RUNATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
RunType.RUNLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.RUNLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS
RunType.RUNLINKS.RUNLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
RunType.RUNLINKS.RUNLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK
RunType.RUNLINKS.RUNLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
RunType.RUNLINKS.RUNLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: runWorkflow.
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: runWorkflow.
runWorkflow(WorkflowInfo, String, String, boolean, String, ArrayList<String>, Registration) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager: runWorkflow.
RunWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries: RunWorkflowResource class.
RunWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.RunWorkflowResource: Constructor for RunWorkflowResource.

S

S3CreateFileURLs - Class in net.sourceforge.seqware.pipeline.modules.utilities: Purpose: This module simply lists files at the S3 URL you provide and creates temporary URLs that can be shared with others.
S3CreateFileURLs() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
S3DeleteFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities: Purpose: This module simply lists files at the S3 URL you provide.
S3DeleteFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
S3ListFiles - Class in net.sourceforge.seqware.pipeline.modules.utilities: Purpose: This module simply lists files at the S3 URL you provide.
S3ListFiles() - Constructor for class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
Sample - Class in net.sourceforge.seqware.common.model
Sample() - Constructor for class net.sourceforge.seqware.common.model.Sample: Constructor for Sample.
sample - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
SAMPLE_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SAMPLE_ATTRIBUTES="Header.SAMPLE_ATTRIBUTES.getTitle()"
SAMPLE_CHILD - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant SAMPLE_CHILD="s_child"
SAMPLE_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SAMPLE_NAME="Header.SAMPLE_NAME.getTitle()"
SAMPLE_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant SAMPLE_PREFIX="sam_"
SAMPLE_SAMPLE - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant SAMPLE_SAMPLE="s_sample"
SAMPLE_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SAMPLE_SWA="Header.SAMPLE_SWA.getTitle()"
SAMPLE_SWID - Static variable in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController: Constant SAMPLE_SWID="sw"
SAMPLE_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SAMPLE_TAG_PREFIX="Header.SAMPLE_TAG_PREFIX.getTitle()"
SampleAttribute - Class in net.sourceforge.seqware.common.model: SampleAttribute generated by hbm2java
SampleAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute: Constructor for SampleAttribute.
SampleAttribute(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute: Constructor for SampleAttribute.
SampleAttribute(int, Sample, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleAttribute: Constructor for SampleAttribute.
sampleattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
sampleAttributeAsDto(SampleAttribute) - Static method in class net.sourceforge.seqware.webservice.dto.Dtos: sampleAttributeAsDto.
SampleAttributeDAO - Interface in net.sourceforge.seqware.common.dao: SampleAttributeDAO interface.
SampleAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: SampleAttributeDAOHibernate class.
SampleAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate
sampleattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
SampleController - Class in net.sourceforge.solexatools.webapp.controller: SampleController
SampleController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController: Constructor for SampleController.
SampleController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleController: Constructor for SampleController.
SampleDAO - Interface in net.sourceforge.seqware.common.dao: SampleDAO interface.
SampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: SampleDAOHibernate class.
SampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: Constructor for SampleDAOHibernate.
sampledescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
SampleDetailsLineItem - Class in net.sourceforge.solexatools.webapp.metamodel: SampleDetailsLineItem class.
SampleDetailsLineItem(SequencerRun, Lane, IUS) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsLineItem: Constructor for SampleDetailsLineItem.
SampleDetailsWorkflowLineItems - Class in net.sourceforge.solexatools.webapp.metamodel: SampleDetailsWorkflowLineItems class.
SampleDetailsWorkflowLineItems(Sample) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems: Constructor for SampleDetailsWorkflowLineItems.
SampleDetailsWorkflowLineItems(Processing) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.SampleDetailsWorkflowLineItems: Constructor for SampleDetailsWorkflowLineItems.
sampleId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
sampleId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
SampleIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries: SampleIdFilesResource class.
SampleIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SampleIdFilesResource: Constructor for SampleIdFilesResource.
SampleIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters: SampleIDFilter class.
SampleIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.SampleIDFilter
SampleIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: SampleIDResource class.
SampleIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleIDResource: Constructor for SampleIDResource.
SampleLink - Class in net.sourceforge.seqware.common.model: SampleLink generated by hbm2java
SampleLink() - Constructor for class net.sourceforge.seqware.common.model.SampleLink: Constructor for SampleLink.
SampleLink(int, Sample, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink: Constructor for SampleLink.
SampleLink(int, Sample, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SampleLink: Constructor for SampleLink.
samplelink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
SampleLinkDAO - Interface in net.sourceforge.seqware.common.dao: SampleLinkDAO interface.
SampleLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: SampleLinkDAOHibernate class.
SampleLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate
samplelinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
SampleList - Class in net.sourceforge.seqware.common.model.lists: SampleList class.
SampleList() - Constructor for class net.sourceforge.seqware.common.model.lists.SampleList: Constructor for SampleList.
samplename - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType
samplepoolref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
sampleRef - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER
sampleref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
sampleRef - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
SampleReportDAO - Interface in net.sourceforge.seqware.common.dao: SampleReportDAO interface.
SampleReportDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: SampleReportDAOHibernate class.
SampleReportDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleReportDAOHibernate
SampleReportRow - Class in net.sourceforge.seqware.common.model: SampleReportRow class.
SampleReportRow() - Constructor for class net.sourceforge.seqware.common.model.SampleReportRow
SampleReportService - Interface in net.sourceforge.seqware.common.business: SampleReportService interface.
SampleReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl: SampleReportServiceImpl class.
SampleReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl
SampleResource - Class in net.sourceforge.seqware.webservice.resources.tables: SampleResource class.
SampleResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SampleResource: Constructor for SampleResource.
SampleSearch - Class in net.sourceforge.seqware.common.model: A search for samples that match a given list of attributes.
SampleSearch() - Constructor for class net.sourceforge.seqware.common.model.SampleSearch
SampleSearchAttribute - Class in net.sourceforge.seqware.common.model: Attributes that are part of a sample search.
SampleSearchAttribute() - Constructor for class net.sourceforge.seqware.common.model.SampleSearchAttribute
SampleSearchDAO - Interface in net.sourceforge.seqware.common.dao: SampleSearchDAO interface.
SampleSearchDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
SampleSearchDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SampleSearchDAOHibernate
SampleSearchDto - Class in net.sourceforge.seqware.webservice.dto
SampleSearchDto() - Constructor for class net.sourceforge.seqware.webservice.dto.SampleSearchDto
SampleSearchService - Interface in net.sourceforge.seqware.common.business: SampleSearchService interface.
SampleSearchServiceImpl - Class in net.sourceforge.seqware.common.business.impl
SampleSearchServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleSearchServiceImpl
SampleService - Interface in net.sourceforge.seqware.common.business: SampleService interface.
SampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl: SampleServiceImpl class.
SampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: Constructor for SampleServiceImpl.
SampleSet - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleSet
SampleSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
SampleSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Constructor for SampleSetupController.
SampleType - Class in net.sourceforge.seqware.queryengine.webservice.model: A Sample defines an isolate of sequenceable material upon which sequencing experiments can be based.
SampleType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType
SampleType.MEMBERS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.MEMBERS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS
SampleType.MEMBERS.MEMBER - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.MEMBERS.MEMBER() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER
SampleType.SAMPLEATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.SAMPLEATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
SampleType.SAMPLELINKS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.SAMPLELINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS
SampleType.SAMPLELINKS.SAMPLELINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.SAMPLELINKS.SAMPLELINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
SampleType.SAMPLENAME - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SampleType.SAMPLENAME() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
SampleValidator - Class in net.sourceforge.solexatools.validation: SampleValidator class.
SampleValidator() - Constructor for class net.sourceforge.solexatools.validation.SampleValidator: Constructor for SampleValidator.
SampleWorkflowRunsController - Class in net.sourceforge.solexatools.webapp.controller: SampleWorkflowRunsController class.
SampleWorkflowRunsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController
SamTools - Class in net.sourceforge.seqware.pipeline.modules: FIXME: if creating pileup requres a .fai file!
SamTools() - Constructor for class net.sourceforge.seqware.pipeline.modules.SamTools
saveAscInSession(HttpServletRequest, String) - Static method in class net.sourceforge.solexatools.util.ControllerUtil: saveAscInSession.
saveAscInSession(HttpServletRequest, String) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: saveAscInSession.
saveFile(MultipartFile, String, Registration) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: saveFile.
saveFile(MultipartFile, String, Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: saveFile.
saveFileForIus(int, int, FileMetadata) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: saveFileForIus.
saveFileForIus(int, int, FileMetadata) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: saveFileForIus.
saveFileForIus(int, int, FileMetadata) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: saveFileForIus.
saveFileForIus(int, int, FileMetadata) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: saveFileForIus.
SaveOpenNodeController - Class in net.sourceforge.solexatools.webapp.controller: SaveOpenNodeController class.
SaveOpenNodeController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Constructor for SaveOpenNodeController.
saveSelectedWorkflowParamValue(HttpServletRequest, Integer, String) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: saveSelectedWorkflowParamValue.
scan(T, S) - Method in interface com.github.seqware.queryengine.plugins.ScanPlugin: Scanner implementation that processes atoms and aggregates results in a new set.
ScanPlugin<T extends Atom,S extends MolSetInterface> - Interface in com.github.seqware.queryengine.plugins: An abstracted map-reduce interface.
scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow: scheduleInstalledBundle.
scheduleInstalledBundle(String, String, ArrayList<String>, boolean, ArrayList<String>, ArrayList<String>, boolean, List<String>) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.WorkflowEngine: scheduleInstalledBundle.
scheduleWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: scheduleWorkflowRun.
schema - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
schema - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
score - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
SCORE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
SEARCH_CASE_SENSITIVE - Static variable in class net.sourceforge.solexatools.webapp.controller.SearchController: Constant SEARCH_CASE_SENSITIVE="search.checked"
SearchController - Class in net.sourceforge.solexatools.webapp.controller: SearchController class.
SearchController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchController: Constructor for SearchController.
SearchResultsController - Class in net.sourceforge.solexatools.webapp.controller: SearchResultsController class.
SearchResultsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsController
SearchResultsListController - Class in net.sourceforge.solexatools.webapp.controller: SearchResultsListController class.
SearchResultsListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Constructor for SearchResultsListController.
SECONDARY_INDEX - Static variable in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker: Constant SECONDARY_INDEX="sIndex.out"
SECONDARY_INDEX_HACK - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant SECONDARY_INDEX_HACK=false
SECONDARY_INDEX_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant SECONDARY_INDEX_PARAM='x'
SecondaryCursorIterator - Class in net.sourceforge.seqware.queryengine.backend.util.iterators: SecondaryCursorIterator class.
SecondaryCursorIterator(SecondaryCursor, TupleBinding, boolean) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: Used to iterate over an entire secondary table with or without duplicates reported
SecondaryCursorIterator(SecondaryCursor, DatabaseEntry, TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.util.iterators.SecondaryCursorIterator: Used to search the secondary table with only duplicates reported back
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
secretKey - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
sector - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
Security - Class in net.sourceforge.solexatools: Security class.
Security() - Constructor for class net.sourceforge.solexatools.Security
SELECTED_FILES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: Constant SELECTED_FILES="selectedLaunchFiles"
SELECTED_NODES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: Constant SELECTED_NODES="launchSelectedNodes"
SELECTED_VALUES - Static variable in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: Constant SELECTED_VALUES="selectedWorkflowParamValueId"
selectExperimentNode(List<String>, Study) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectExperimentNode.
SelectInputController - Class in net.sourceforge.solexatools.webapp.controller: SelectInputController class.
SelectInputController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController: Constructor for SelectInputController.
SelectInputController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputController: Constructor for SelectInputController.
SelectInputListController - Class in net.sourceforge.solexatools.webapp.controller: SelectInputListController class.
SelectInputListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Constructor for SelectInputListController.
selectIUSNode(List<String>, Sample) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectIUSNode.
selectProcessingNode(List<String>, WorkflowRun) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectProcessingNode.
selectProcessingNode(List<String>, Processing) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectProcessingNode.
selectProcessingNode(List<String>, Lane) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectProcessingNode.
selectProcessingNode(List<String>, IUS) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectProcessingNode.
selectSampleNode(List<String>, Experiment) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectSampleNode.
selectStudyNode(List<String>, List<Study>) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectStudyNode.
selectWorkflowRunNode(List<String>, List<WorkflowRun>) - Static method in class net.sourceforge.solexatools.util.BulkUtil: selectWorkflowRunNode.
separateFiles(List<ReturnValue>, String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
SEPARATOR - Static variable in class com.github.seqware.queryengine.impl.StorageInterface: Constant SEPARATOR="."
SEPARATOR - Static variable in class com.github.seqware.queryengine.model.Tag: Constant SEPARATOR="::"
SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.ChangeNumberPopupPageController: Constant SEPARATOR="java.io.File.separator"
SEPARATOR - Static variable in class net.sourceforge.solexatools.webapp.controller.DeleteLoadedIndexPageController: Constant SEPARATOR="java.io.File.separator"
SEQ_RUN_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant SEQ_RUN_ID="seq_run_id"
SEQUENCER_RUN_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SEQUENCER_RUN_ATTRIBUTES="Header.SEQUENCER_RUN_ATTRIBUTES.getTitl"{trunked}
SEQUENCER_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SEQUENCER_RUN_NAME="Header.SEQUENCER_RUN_NAME.getTitle()"
SEQUENCER_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SEQUENCER_RUN_SWA="Header.SEQUENCER_RUN_SWA.getTitle()"
SEQUENCER_RUN_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant SEQUENCER_RUN_TAG_PREFIX="Header.SEQUENCER_RUN_TAG_PREFIX.getTitl"{trunked}
SEQUENCER_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant: Constant SEQUENCER_VIEW="redirect:/sequencerRunList.htm"
SequencerRun - Class in net.sourceforge.seqware.common.model
SequencerRun() - Constructor for class net.sourceforge.seqware.common.model.SequencerRun: Constructor for SequencerRun.
SequencerRunAttribute - Class in net.sourceforge.seqware.common.model: SequencerRunAttribute generated by Morgan Taschuk
SequencerRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute: Constructor for SequencerRunAttribute.
SequencerRunAttribute(int, SequencerRunWizardDTO) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute: Constructor for SequencerRunAttribute.
SequencerRunAttribute(int, SequencerRunWizardDTO, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.SequencerRunAttribute: Constructor for SequencerRunAttribute.
SequencerRunController - Class in net.sourceforge.solexatools.webapp.controller: SequencerRunController
SequencerRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Constructor for SequencerRunController.
SequencerRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Constructor for SequencerRunController.
SequencerRunControllerDTO - Class in net.sourceforge.solexatools.webapp.controller: SequencerRunController
SequencerRunControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Constructor for SequencerRunControllerDTO.
SequencerRunControllerDTO(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Constructor for SequencerRunControllerDTO.
SequencerRunDAO - Interface in net.sourceforge.seqware.common.dao: SequencerRunDAO interface.
SequencerRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: SequencerRunDAOHibernate class.
SequencerRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: Constructor for SequencerRunDAOHibernate.
SequencerRunDTO - Class in net.sourceforge.seqware.common.model
SequencerRunDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunDTO: Constructor for SequencerRunDTO.
SequencerRunHtmlUtil - Class in net.sourceforge.solexatools.util: SequencerRunHtmlUtil class.
SequencerRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.SequencerRunHtmlUtil
SequencerRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries: SequencerRunIdFilesResource class.
SequencerRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunIdFilesResource: Constructor for SequencerRunIdFilesResource.
SequencerRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: SequencerRunIDResource class.
SequencerRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunIDResource: Constructor for SequencerRunIDResource.
SequencerRunList - Class in net.sourceforge.seqware.common.model.lists: SequencerRunList class.
SequencerRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.SequencerRunList: Constructor for SequencerRunList.
SequencerRunListController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
SequencerRunListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListController: Constructor for SequencerRunListController.
SequencerRunListDetailsController - Class in net.sourceforge.solexatools.webapp.controller: SequencerRunListDetailsController class.
SequencerRunListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Constructor for SequencerRunListDetailsController.
SequencerRunReport - Class in net.sourceforge.seqware.common.hibernate: SequencerRunReport class.
SequencerRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport
SequencerRunReport.Row - Class in net.sourceforge.seqware.common.hibernate
SequencerRunReport.Row(Date, String, String, String, String, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
SequencerRunReporter - Class in net.sourceforge.seqware.pipeline.plugins: SequencerRunReporter class.
SequencerRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SequencerRunReporter: Constructor for SequencerRunReporter.
SequencerRunReportId - Class in net.sourceforge.seqware.common.model: SequencerRunReportId class.
SequencerRunReportId() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunReportId
SequencerRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries: SequencerRunReportResource class.
SequencerRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.SequencerRunReportResource: Constructor for SequencerRunReportResource.
SequencerRunReportSetupController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController
SequencerRunReportTableController - Class in net.sourceforge.solexatools.webapp.controller
SequencerRunReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController
SequencerRunResource - Class in net.sourceforge.seqware.webservice.resources.tables: SequencerRunResource class.
SequencerRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.SequencerRunResource: Constructor for SequencerRunResource.
SequencerRunService - Interface in net.sourceforge.seqware.common.business: SequencerRunService interface.
SequencerRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl: SequencerRunServiceImpl class.
SequencerRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: Constructor for SequencerRunServiceImpl.
SequencerRunSetupController - Class in net.sourceforge.solexatools.webapp.controller: SequencingRunSetupController
SequencerRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController: Constructor for SequencerRunSetupController.
SequencerRunSetupControllerDTO - Class in net.sourceforge.solexatools.webapp.controller: SequencingRunSetupController
SequencerRunSetupControllerDTO() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO: Constructor for SequencerRunSetupControllerDTO.
SequencerRunValidator - Class in net.sourceforge.solexatools.validation: SequencerRunValidator class.
SequencerRunValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunValidator: Constructor for SequencerRunValidator.
SequencerRunWizardController - Class in net.sourceforge.solexatools.webapp.controller: SequencerRunWizardController class.
SequencerRunWizardController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Constructor for SequencerRunWizardController.
SequencerRunWizardController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Constructor for SequencerRunWizardController.
SequencerRunWizardDTO - Class in net.sourceforge.seqware.common.model: SequencerRunWizardDTO class.
SequencerRunWizardDTO() - Constructor for class net.sourceforge.seqware.common.model.SequencerRunWizardDTO: Constructor for SequencerRunWizardDTO.
SequencerRunWizardSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
SequencerRunWizardSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController: Constructor for SequencerRunWizardSetupController.
SequencerRunWizardValidator - Class in net.sourceforge.solexatools.validation: SequencerRunWizardValidator class.
SequencerRunWizardValidator() - Constructor for class net.sourceforge.solexatools.validation.SequencerRunWizardValidator: Constructor for SequencerRunWizardValidator.
sequencers - Static variable in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq: Constant sequencers="{ Solexa_1G_Genome_Analyzer, Illumina_G"{trunked}
sequencers - Static variable in class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2: Constant sequencers="{ Solexa_1G_Genome_Analyzer, Illumina_G"{trunked}
sequencers - Static variable in class net.sourceforge.seqware.pipeline.modules.srf2fastq: Constant sequencers="{ illumina-ga2, solid-3 }"
sequencespace - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS
sequencingprotocol - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
SEQWARE_SETTINGS_PROPERTY - Static variable in class net.sourceforge.seqware.common.util.configtools.ConfigTools: Constant SEQWARE_SETTINGS_PROPERTY="SEQWARE_SETTINGS"
SeqwareAccessionIDResource - Class in net.sourceforge.seqware.webservice.resources: SeqwareAccessionIDResource class.
SeqwareAccessionIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionIDResource
SeqwareAccessionResource - Class in net.sourceforge.seqware.webservice.resources: SeqwareAccessionResource class.
SeqwareAccessionResource() - Constructor for class net.sourceforge.seqware.webservice.resources.SeqwareAccessionResource
SeqWareBase - Class in net.sourceforge.seqware.queryengine.backend.util: SeqWareBase class.
SeqWareBase() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase
SeqWareCursor - Class in net.sourceforge.seqware.queryengine.backend.util: SeqWareCursor class.
SeqWareCursor() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareCursor
SeqwareException - Exception in net.sourceforge.seqware.common.err: Created by IntelliJ IDEA.
SeqwareException() - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException: Constructor for SeqwareException.
SeqwareException(String) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException: Constructor for SeqwareException.
SeqwareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException: Constructor for SeqwareException.
SeqwareException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SeqwareException: Constructor for SeqwareException.
SeqWareException - Exception in net.sourceforge.seqware.queryengine.backend.util: SeqWareException class.
SeqWareException() - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException: Constructor for SeqWareException.
SeqWareException(String) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException: Constructor for SeqWareException.
SeqWareException(Throwable) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException: Constructor for SeqWareException.
SeqWareException(String, Throwable) - Constructor for exception net.sourceforge.seqware.queryengine.backend.util.SeqWareException: Constructor for SeqWareException.
SeqwareExitCode - Class in net.sourceforge.seqware.common.err: Created by IntelliJ IDEA.
SeqwareExitCode() - Constructor for class net.sourceforge.seqware.common.err.SeqwareExitCode
SeqWareIterable<T> - Interface in com.github.seqware.queryengine.util: All SeqWare iterable collections should be easily countable too
SeqWareIterator<T> - Class in com.github.seqware.queryengine.util: Iterator implementation that deals with database iterators that require explicit closing.
SeqWareIterator() - Constructor for class com.github.seqware.queryengine.util.SeqWareIterator
SeqWareIterator - Interface in net.sourceforge.seqware.queryengine.backend.util: SeqWareIterator interface.
SeqWareQueryLanguageLexer - Class in com.github.seqware.queryengine.kernel.output: SeqWareQueryLanguageLexer class.
SeqWareQueryLanguageLexer() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constructor for SeqWareQueryLanguageLexer.
SeqWareQueryLanguageLexer(CharStream) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constructor for SeqWareQueryLanguageLexer.
SeqWareQueryLanguageLexer(CharStream, RecognizerSharedState) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constructor for SeqWareQueryLanguageLexer.
SeqWareQueryLanguageLexerWrapper - Class in com.github.seqware.queryengine.kernel: SeqWareQueryLanguageLexerWrapper class.
SeqWareQueryLanguageLexerWrapper(CharStream) - Constructor for class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageLexerWrapper: Constructor for SeqWareQueryLanguageLexerWrapper.
SeqWareQueryLanguageParser - Class in com.github.seqware.queryengine.kernel.output: SeqWareQueryLanguageParser class.
SeqWareQueryLanguageParser(TokenStream) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constructor for SeqWareQueryLanguageParser.
SeqWareQueryLanguageParser(TokenStream, RecognizerSharedState) - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constructor for SeqWareQueryLanguageParser.
SeqWareQueryLanguageParser.comment_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.comment_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comment_return
SeqWareQueryLanguageParser.comparison_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.comparison_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.comparison_return
SeqWareQueryLanguageParser.constant_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.constant_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constant_return
SeqWareQueryLanguageParser.constraint_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.constraint_return
SeqWareQueryLanguageParser.high_precedence_constraint_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.high_precedence_constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.high_precedence_constraint_return
SeqWareQueryLanguageParser.identifier_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.identifier_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.identifier_return
SeqWareQueryLanguageParser.key_value_function_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.key_value_function_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.key_value_function_return
SeqWareQueryLanguageParser.literal_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.literal_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.literal_return
SeqWareQueryLanguageParser.low_precedence_constraint_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.low_precedence_constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.low_precedence_constraint_return
SeqWareQueryLanguageParser.nested_constraint_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.nested_constraint_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.nested_constraint_return
SeqWareQueryLanguageParser.query_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.query_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.query_return
SeqWareQueryLanguageParser.three_param_predicate_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.three_param_predicate_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.three_param_predicate_return
SeqWareQueryLanguageParser.two_param_predicate_return - Class in com.github.seqware.queryengine.kernel.output
SeqWareQueryLanguageParser.two_param_predicate_return() - Constructor for class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser.two_param_predicate_return
SeqWareQueryLanguageParserWrapper - Class in com.github.seqware.queryengine.kernel: SeqWareQueryLanguageParserWrapper class.
SeqWareQueryLanguageParserWrapper(TokenStream) - Constructor for class com.github.seqware.queryengine.kernel.SeqWareQueryLanguageParserWrapper: Constructor for SeqWareQueryLanguageParserWrapper.
SeqWareSettings - Class in net.sourceforge.seqware.queryengine.backend.util: SeqWareSettings class.
SeqWareSettings() - Constructor for class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings
SeqWareVerifier - Class in net.sourceforge.seqware.queryengine.webservice.security: SeqWareVerifier class.
SeqWareVerifier() - Constructor for class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
SeqWareWebServiceApplication - Class in net.sourceforge.seqware.queryengine.webservice.controller: SeqWareWebServiceApplication class.
SeqWareWebServiceApplication() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication
SeqWareWebServiceApplication.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller: http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
SeqWareWebServiceApplication.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
SeqWareWebServiceApplication.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplication.OptionalSlashRedirect
SeqWareWebServiceApplicationVersion - Class in net.sourceforge.seqware.queryengine.webservice.controller: SeqWareWebServiceApplicationVersion class.
SeqWareWebServiceApplicationVersion() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect - Class in net.sourceforge.seqware.queryengine.webservice.controller: http://restlet-discuss.1400322.n2.nabble.com/Proper-handling-of-at-the-end-of-the-requested-URI-td5819896.html
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect(Context) - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
SeqWareWebServiceApplicationVersion.OptionalSlashRedirect() - Constructor for class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceApplicationVersion.OptionalSlashRedirect
SeqWareWebServiceMain - Class in net.sourceforge.seqware.queryengine.webservice.controller: SeqWareWebServiceMain class.
SERIALIZATIONCONSTANT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
SERIALIZATIONCONSTANT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
SerializationInterface - Interface in com.github.seqware.queryengine.impl: This simply extracts the serialization of bytes[] to atoms and vice versa.
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.ApacheSerialization: Given an atom, get back an array of bytes
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.KryoSerialization: Given an atom, get back an array of bytes
serialize(Atom) - Method in class com.github.seqware.queryengine.impl.ProtobufSerialization: Given an atom, get back an array of bytes
serialize(Atom) - Method in interface com.github.seqware.queryengine.impl.SerializationInterface: Given an atom, get back an array of bytes
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomsToTarget(T...) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomsToTarget(Atom...) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Generically serialize a batch of Atoms, all of the same class This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.HBaseStorage: Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.NonPersistentStorage: Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.StorageInterface: Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeAtomToTarget(Atom) - Method in class com.github.seqware.queryengine.impl.TmpFileStorage: Generically serialize an Atom into the interface This method is also responsible for ensuring that the atom's backendTimestamp is populated
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag: Adag object serialize to element and all its sub objects serialize to sub element
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn
serializeXML() - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
set - Variable in class com.github.seqware.queryengine.model.impl.inMemory.AbstractInMemorySet
set(T) - Method in class com.github.seqware.queryengine.util.LazyReference: Set the lazy reference of the object with an actual object.
setABISOLID(ExperimentType.PLATFORM.ABISOLID) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Sets the value of the abisolid property.
setAbstractStr(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field abstractStr.
setABUNDANCEMEASUREMENT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the abundancemeasurement property.
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field accession.
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Organism: Setter for the field accession.
setAccession(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field accession.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Sets the value of the accession property.
setAccession(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the accession property.
setAcl(QueryEngine.ACLPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
setAcl(QueryEngine.ACLPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
setACTIONS(SubmissionType.ACTIONS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the actions property.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareFile: Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareLane: Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareSample: Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareStudy: Setter for the field active.
setActive(Boolean) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Setter for the field active.
setAdapters(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field adapters.
setAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Setter for the field adapterSpec.
setADAPTERSPEC(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC: Sets the value of the adapterspec property.
setADD(SubmissionType.ACTIONS.ACTION.ADD) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Sets the value of the add property.
setAddedSurcharge(Double) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field addedSurcharge.
setAdditionalAttribute(String, Feature.AdditionalAttributeType) - Method in class com.github.seqware.queryengine.model.Feature: Sets an additional attribute not covered by GVF.
setAdhoctagset(SGID) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field adhoctagset.
setAgent(String) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field agent.
setAlgo(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: set the job algorithm
setAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field algorithm.
setAlgorithm(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field algorithm.
setAlgorithm(String) - Method in class net.sourceforge.seqware.pipeline.module.Module: Setter for the field algorithm.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field alias.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Sets the value of the alias property.
setAlias(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the alias property.
setAlign(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
setAllItems(String) - Method in class net.sourceforge.solexatools.util.PageInfo: Setter for the field allItems.
setANALYSISATTRIBUTES(AnalysisType.ANALYSISATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the analysisattributes property.
setAnalysisCenter(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the analysisCenter property.
setANALYSISFILES(AnalysisType.ANALYSISFILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the analysisfiles property.
setAnalysisIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setAnalysisIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setANALYSISLINKS(AnalysisType.ANALYSISLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the analysislinks property.
setAnalysisPluginACL(ACL, AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setAnalysisPluginACL.
setAnalysisSetACL(ACL, AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setAnalysisSetACL.
setANALYSISTYPE(AnalysisType.ANALYSISTYPE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the analysistype property.
setAnonymizedName(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field anonymizedName.
setANONYMIZEDNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME: Sets the value of the anonymizedname property.
setApplicationContext(ApplicationContext) - Method in class net.sourceforge.seqware.pipeline.runner.Runner2: setApplicationContext.
setArch(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
setArgs(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest.TestThread
setArguments(List<String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
setAsText(String) - Method in class net.sourceforge.solexatools.validation.CustomIntegerEditor
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
setAtom(QESupporting.FeatureAtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setAtom(QESupporting.FeatureAtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setAtom(QESupporting.AtomPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setAtom(QESupporting.AtomPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setAtom(Atom) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
setAttribute(String, String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: setAttribute.
setAttributes(Map<String, String>) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field attributes.
setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field attributes.
setAttributes(Set<AttributeDto>) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto: Setter for the field attributes.
setBackendTimestamp(Date) - Method in class com.github.seqware.queryengine.util.SGID: Setter for the field backendTimestamp.
setBarcode(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field barcode.
setBarcodeSeqence(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER: Sets the value of the barcodeSeqence property.
setBaseCaller(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field baseCaller.
setBASECALLER(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS: Sets the value of the basecaller property.
setBASECALLS(ExperimentType.PROCESSING.BASECALLS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING: Sets the value of the basecalls property.
setBaseCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field baseCoord.
setBASECOORD(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Sets the value of the basecoord property.
setBaseDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field baseDir.
setBaseIniFile(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field baseIniFile.
setBaseQualities(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field baseQualities.
setBatch_size(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field batch_size.
setBinSize(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field binSize.
setBinSize(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field binSize.
setBlockCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field blockCount.
setBlockSizes(int[]) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field blockSizes.
setBlockStarts(int[]) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field blockStarts.
setBrokerName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the brokerName property.
setCacheSize(long) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field cacheSize.
setCalledBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field calledBase.
setCalledBaseCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field calledBaseCount.
setCalledBaseCountForward(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field calledBaseCountForward.
setCalledBaseCountReverse(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field calledBaseCountReverse.
setCallOne(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field callOne.
setCallTwo(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field callTwo.
setCascade(boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
setCell(List<String>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.Cells
setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field centerName.
setCenterName(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field centerName.
setCenterName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the centerName property.
setCENTERNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Sets the value of the centername property.
setCenterName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the centerName property.
setCenterProjectName(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field centerProjectName.
setCENTERPROJECTNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Sets the value of the centerprojectname property.
setChecksum(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE: Sets the value of the checksum property.
setChecksumMethod(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE: Sets the value of the checksumMethod property.
setChildren(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field children.
setChildren(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field children.
setChildrenUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field childrenUrls.
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Setter for the field childSample.
setChildSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field childSample.
setClassesDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field classesDir.
setClientNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field clientNotes.
setCode(String) - Method in class net.sourceforge.seqware.common.model.Organism: Setter for the field code.
setCode(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto: Setter for the field code.
setCodingStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field codingStart.
setCodingStop(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field codingStop.
setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field colorMatrix.
setColorMatrix(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field colorMatrix.
setCOLORMATRIX(ExperimentType.PLATFORM.ABISOLID.COLORMATRIX) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Sets the value of the colormatrix property.
setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field colorMatrixCode.
setColorMatrixCode(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field colorMatrixCode.
setCOLORMATRIXCODE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Sets the value of the colormatrixcode property.
setCommand(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field command.
setCommand(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field command.
setCommand(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field command.
setCommand(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
setCommand(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: set the job command
setCOMMONNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME: Sets the value of the commonname property.
setCompleted(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field completed.
setCompressed(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field compressed.
setCompressed(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field compressed.
setCompute(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
setComputeReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field computeReq.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.decider.Decider: Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Let's you set the config this object should use.
setConfig(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Let's you set the config this object should use.
setConfigPath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field configPath.
setConfigs(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set the key-value properties for workflow
setConfirmEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO: Setter for the field confirmEmailAddress.
setConfirmPassword(String) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO: Setter for the field confirmPassword.
setConnectionString(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field connectionString.
setConsensusAveSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field consensusAveSeqQuality.
setConsensusBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field consensusBase.
setConsensusCallQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field consensusCallQuality.
setConsensusMaxSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field consensusMaxSeqQuality.
setConstructionProtocol(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field constructionProtocol.
setCONTACTS(SubmissionType.CONTACTS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the contacts property.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition: Setter for the field contig.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel: Setter for the field contig.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field contig.
setContig(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Setter for the field contig.
setCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: Setter for the field count.
setCountFile(Integer) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field countFile.
setCoverage(HashMap<Integer, Integer>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: Setter for the field coverage.
setCreateConsequenceAnnotationDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field createConsequenceAnnotationDB.
setCreateCoverageDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field createCoverageDB.
setCreated(Date) - Method in class net.sourceforge.seqware.common.model.SampleSearch: Setter for the field created.
setCreateDbSNPAnnotationDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field createDbSNPAnnotationDB.
setCreateMismatchDB(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field createMismatchDB.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field createTimestamp.
setCreateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field createTimestamp.
setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field createTimeStamp.
setCreateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field createTimeStamp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile: Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane: Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Setter for the field createTstmp.
setCreateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample: Setter for the field createTstmp.
setCriteria(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController: Setter for the field criteria.
setCurrentSelectedFiles(HttpServletRequest, List<File>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: setCurrentSelectedFiles.
setCurrentSelectedNodes(HttpServletRequest, List<String>) - Static method in class net.sourceforge.solexatools.util.LaunchWorkflowUtil: setCurrentSelectedNodes.
setCurrentWorkingDir(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field currentWorkingDir.
setCwd(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field cwd.
setCycleCoord(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field cycleCoord.
setCYCLECOORD(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Sets the value of the cyclecoord property.
setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field cycleCount.
setCycleCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field cycleCount.
setCYCLECOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Sets the value of the cyclecount property.
setCYCLECOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA: Sets the value of the cyclecount property.
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field cycleDescriptor.
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field cycleDescriptor.
setCycleDescriptor(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field cycleDescriptor.
setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field cycles.
setCycles(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field cycles.
setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field cycleSequence.
setCycleSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field cycleSequence.
setCYCLESEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA: Sets the value of the cyclesequence property.
setData(ArrayList) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: Setter for the field data.
setDatabase(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field database.
setDataDecryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Sets data decryption key.
setDataEncryptionKeyString(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Sets data encryption key.
setDate(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setDate(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
setDate(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set the pre-defined date variable
setDax(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field dax.
setDaxDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
setDaysUntilDue(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field daysUntilDue.
setDb(Connection) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.IUSLink: Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.LaneLink: Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.SampleLink: Setter for the field db.
setDb(String) - Method in class net.sourceforge.seqware.common.model.StudyLink: Setter for the field db.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK: Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK: Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK: Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK: Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK: Sets the value of the db property.
setDB(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK: Sets the value of the db property.
setDbmd(DatabaseMetaData) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Setter for the field dbmd.
setDebug(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareBase: Setter for the field debug.
setDecodeMethod(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Setter for the field decodeMethod.
setDefaultValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field defaultValue.
setDENOVOASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the denovoassembly property.
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
setDescription(String) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Platform: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.StudyType: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setDescription(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field description.
setDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the description property.
setDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Sets the value of the description property.
setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Setter for the field description.
setDescription(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field description.
setDESCRIPTOR(StudyType.DESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Sets the value of the descriptor property.
setDESIGN(ExperimentType.DESIGN) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the design property.
setDESIGNDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Sets the value of the designdescription property.
setDibase(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR: Sets the value of the dibase property.
setDisplay(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field display.
setDisplay(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.FileType: Setter for the field displayName.
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field displayName.
setDisplayName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Setter for the field displayName.
setDisplayName(String) - Method in class net.sourceforge.solexatools.util.SummaryLine: Setter for the field displayName.
setDisplayValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field displayValue.
setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.RegistrationDTO: Setter for the field domainObject.
setDomainObject(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO: Setter for the field domainObject.
setEarliestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport: Set the value of earliestDate.
setEmail(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Setter for the field email.
setEmailAddress(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setEmailAddress(String) - Method in class com.github.seqware.queryengine.model.User.Builder
setEmailAddress(String) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field emailAddress.
setEnd(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field end.
setEndDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field endDate.
setEndPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo: Setter for the field endPage.
setEntityUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Setter for the field entityUrl.
setENTREZLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK: Sets the value of the entrezlink property.
setENTREZLINK(ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK: Sets the value of the entrezlink property.
setENTREZLINK(RunType.RUNLINKS.RUNLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK: Sets the value of the entrezlink property.
setENTREZLINK(SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK: Sets the value of the entrezlink property.
setENTREZLINK(StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK: Sets the value of the entrezlink property.
setErrorCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field errorCount.
setExecutionEnv(Environment.ExecutionEnvironment) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment: set the execution environment
setExistingStudyType(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE: Sets the value of the existingStudyType property.
setExistingType(StudyType) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field existingType.
setExistingTypeInt(Integer) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field existingTypeInt.
setExitCode(int) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException: Setter for the field exitCode.
setExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field exitStatus.
setExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field exitStatus.
setExpectedBaseCall(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field expectedBaseCall.
setEXPECTEDBASECALL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Sets the value of the expectedbasecall property.
setExpectedNumberReads(Long) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expectedNumberReads.
setExpectedNumberReads(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the expectedNumberReads property.
setExpectedNumberRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expectedNumberRuns.
setExpectedNumberRuns(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the expectedNumberRuns property.
setExpectedNumberSpots(Long) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expectedNumberSpots.
setExpectedNumberSpots(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the expectedNumberSpots property.
setExpectedNumReads(Integer) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field expectedNumReads.
setExpectedNumRuns(Integer) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field expectedNumRuns.
setExpectedNumSpots(Integer) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field expectedNumSpots.
setExpenseId(Integer) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field expenseId.
setExpenses(Set<Expense>) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field expenses.
setExpenseType(String) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field expenseType.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field experiment.
setExperiment(Experiment) - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Setter for the field experiment.
setExperiment(Experiment, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setExperiment.
setExperimentAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Setter for the field experimentAttributeId.
setExperimentAttributes(Set<ExperimentAttribute>) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field experimentAttributes.
setEXPERIMENTATTRIBUTES(ExperimentType.EXPERIMENTATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the experimentattributes property.
setExperimentDAO(ExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: setExperimentDAO.
setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: setExperimentDAO.
setExperimentDAO(ExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Setter for the field experimentDAO.
setExperimentId(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field experimentId.
setExperimentLibraryDesign(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field experimentLibraryDesign.
setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: setExperimentLibraryDesignDAO.
setExperimentLibraryDesignDAO(ExperimentLibraryDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: setExperimentLibraryDesignDAO.
setExperimentLibraryDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field experimentLibraryDesignId.
setExperimentLibraryDesignService(ExperimentLibraryDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field experimentLibraryDesignService.
setExperimentLinkId(int) - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Setter for the field experimentLinkId.
setExperimentLinks(Set<ExperimentLink>) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field experimentLinks.
setEXPERIMENTLINKS(ExperimentType.EXPERIMENTLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the experimentlinks property.
setEXPERIMENTREF(AnalysisType.PARENT.EXPERIMENTREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Sets the value of the experimentref property.
setEXPERIMENTREF(RunType.EXPERIMENTREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the experimentref property.
setExperiments(Set<Experiment>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field experiments.
setExperiments(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field experiments.
setExperimentService(ExperimentService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field experimentService.
setExperimentService(ExperimentService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field experimentService.
setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field experimentSpotDesign.
setExperimentSpotDesign(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field experimentSpotDesign.
setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService: setExperimentSpotDesignDAO.
setExperimentSpotDesignDAO(ExperimentSpotDesignDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl: setExperimentSpotDesignDAO.
setExperimentSpotDesignId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Setter for the field experimentSpotDesignId.
setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: setExperimentSpotDesignReadSpecDAO.
setExperimentSpotDesignReadSpecDAO(ExperimentSpotDesignReadSpecDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: setExperimentSpotDesignReadSpecDAO.
setExperimentSpotDesignReadSpecId(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field experimentSpotDesignReadSpecId.
setExperimentSpotDesignReadSpecService(ExperimentSpotDesignReadSpecService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field experimentSpotDesignReadSpecService.
setExperimentSpotDesignService(ExperimentSpotDesignService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field experimentSpotDesignService.
setExperimentSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setExpiryTime(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB.Builder
setExpLibDesignDesc(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expLibDesignDesc.
setExpLibDesignName(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expLibDesignName.
setExpLibDesignProtocol(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expLibDesignProtocol.
setExpLibDesignSelection(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expLibDesignSelection.
setExpLibDesignSource(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expLibDesignSource.
setExpLibDesignStrategy(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expLibDesignStrategy.
setExpSpotDesignAdapterSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expSpotDesignAdapterSpec.
setExpSpotDesignReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expSpotDesignReadsPerSpot.
setExpSpotDesignTagSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field expSpotDesignTagSpec.
setExtension(String) - Method in class net.sourceforge.seqware.common.model.FileType: Setter for the field extension.
setExternalId(String) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field externalId.
setExternalSerializationVersion(int) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Setter for the field externalSerializationVersion.
setFactoryBackendType(SWQEFactory.Model_Type, SWQEFactory.Storage_Type, SWQEFactory.Serialization_Type) - Static method in class com.github.seqware.queryengine.factory.SWQEFactory: Used only by testing to override the back-end type
setFailed(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field failed.
setFastqConvNum(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field fastqConvNum.
setFastqConvNum(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field fastqConvNum.
setFeature(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field feature.
setFeatureACL(ACL, Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setFeatureACL.
setFeatures(int, QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
setFeatures(int, QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB.Builder
setFeatures(int, QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setFeatures(int, QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setFeatureSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
setFeatureSet(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
setFeatureSetACL(ACL, Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setFeatureSetACL.
setFeatureSetID(SGID) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field featureSetID.
setFeatureSetIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setFeatureSetIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setFile(MultipartFile) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field file.
setFile(File) - Method in class net.sourceforge.seqware.common.model.FileAttribute: Setter for the field file.
setFile(File) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field file.
setFile(File) - Method in class net.sourceforge.seqware.common.model.ShareFile: Setter for the field file.
setFile(File) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Setter for the field file.
setFileAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileAttribute: Setter for the field fileAttributeId.
setFileAttributes(Set<FileAttribute>) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field fileAttributes.
setFileDAO(FileDAO) - Method in interface net.sourceforge.seqware.common.business.FileService: setFileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: setFileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: Setter for the field fileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileDAO(FileDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: Sets a private member variable with an instance of an implementation of FileDAO.
setFileForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setFileForSequrncerRun.
setFileForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setFileForStudy.
setFileForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setFileForWorkflowRun.
setFileForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setFileForWorkflowRunRunning.
setFileId(Integer) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field fileId.
setFileMetaType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field fileMetaType.
setFileMetaType(String) - Method in class net.sourceforge.solexatools.util.SummaryLine: Setter for the field fileMetaType.
setFilename(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setFilename(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE: Sets the value of the filename property.
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE: Sets the value of the filename property.
setFilename(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE: Sets the value of the filename property.
setFileOne(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field fileOne.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setFilePath(File) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setFilePath(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field filePath.
setFilePath(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Setter for the field filePath.
setFileReportDAO(FileReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileReportServiceImpl: Setter for the field fileReportDAO.
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Setter for the field fileReportService.
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Setter for the field fileReportService.
setFileReportService(FileReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Setter for the field fileReportService.
setFiles(Set<File>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field files.
setFiles(List<File>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field files.
setFiles(ArrayList<FileMetadata>) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field files.
setFILES(RunType.DATABLOCK.FILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the files property.
setFILES(SubmissionType.FILES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the files property.
setFiles(List<File>) - Method in class net.sourceforge.solexatools.util.SummaryLine: Setter for the field files.
setFiles_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field files_url.
setFilesArray(ArrayList<File>) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: Setter for the field filesArray.
setFileService(FileService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloaderController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloaderController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.FileSetupController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.LoadIndexPageController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field fileService.
setFileService(FileService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Setter for the field fileService.
setFileStatus(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setFileSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setFileTwo(MultipartFile) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field fileTwo.
setFileTwoURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field fileTwoURL.
setFileType(FileType) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field fileType.
setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field fileType.
setFileType(FileType) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field fileType.
setFiletype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISFILES.FILE: Sets the value of the filetype property.
setFiletype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK.FILES.FILE: Sets the value of the filetype property.
setFileTypeDAO(FileTypeDAO) - Method in interface net.sourceforge.seqware.common.business.FileTypeService: setFileTypeDAO.
setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl: setFileTypeDAO.
setFileTypeDAO(FileTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Setter for the field fileTypeDAO.
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field fileTypeId.
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.FileType: Setter for the field fileTypeId.
setFileTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field fileTypeId.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator: Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Setter for the field fileTypeService.
setFileTypeService(FileTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController: Setter for the field fileTypeService.
setFileUploadService(FileUploadService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field fileUploadService.
setFileURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field fileURL.
setFileURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field fileURL.
setFinalized(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field finalized.
setFinishedTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field finishedTimestamp.
setFirstName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setFirstName(String) - Method in class com.github.seqware.queryengine.model.User.Builder
setFirstName(String) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field firstName.
setFirstName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Setter for the field firstName.
setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field flowCount.
setFlowCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field flowCount.
setFLOWCOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS: Sets the value of the flowcount property.
setFLOWCOUNT(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454: Sets the value of the flowcount property.
setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field flowSequence.
setFlowSequence(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field flowSequence.
setFLOWSEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS: Sets the value of the flowsequence property.
setFLOWSEQUENCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454: Sets the value of the flowsequence property.
setFolderStore(String) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field folderStore.
setFolderStore(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field folderStore.
setForceCopy(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile: when forceCopy is true, it will pass "--forcecopy" argument to provisionFileJob
setForceRunAll(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setFormatCode(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the formatCode property.
setFrame(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field frame.
setFriendlyRowkey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Analysis.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder: Set a friendly rowKey for the atom to be built.
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Reference.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.model.User.Builder
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.util.FSGID: Setter for the field friendlyRowKey.
setFriendlyRowKey(String) - Method in class com.github.seqware.queryengine.util.SGID: Setter for the field friendlyRowKey.
setFullyPaid(boolean) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field fullyPaid.
setFuzzyStartPositionMax(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field fuzzyStartPositionMax.
setFuzzyStopPositionMin(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field fuzzyStopPositionMin.
setGcrOutputFile(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
setGcrSkipIfMissing(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
setGcrSkipIfOutputExists(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
setGeneChr(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field geneChr.
setGeneId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field geneId.
setGeneId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field geneId.
setGenomeId(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field genomeId.
setGenomicSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field genomicSequence.
setGroup(Group) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder: Set the group permissions
setGroup(SGID) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder: Set the SGID for the group permissions
setGroup(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field group.
setGroupACL(ACL, Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setGroupACL.
setGrp(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
setGrp(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
setGrps(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setGrps(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setHandle(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the handle property.
setHasMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
setHasMetadataWriteback(boolean) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: job specific metadata is not supported yet
setHeader(FindAllTheFiles.Header) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setHELICOS(ExperimentType.PLATFORM.HELICOS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Sets the value of the helicos property.
setHOLD(SubmissionType.ACTIONS.ACTION.HOLD) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Sets the value of the hold property.
setHoldForPeriod(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Sets the value of the holdForPeriod property.
setHoldUntilDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Sets the value of the holdUntilDate property.
setHost(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field host.
setHost(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field host.
setHost(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field host.
setHtml(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field html.
setHtml(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field html.
setHtml(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field html.
setHYBRIDASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the hybridassembly property.
setId(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setId(Integer) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.IUSLink: Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.LaneLink: Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.SampleLink: Setter for the field id.
setId(String) - Method in class net.sourceforge.seqware.common.model.StudyLink: Setter for the field id.
setId(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob: set the job id
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: setId.
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model: setId.
setId(String) - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface: setId.
setId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.StringId: Setter for the field id.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.ENTREZLINK: Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK: Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.ENTREZLINK: Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.ENTREZLINK: Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.ENTREZLINK: Sets the value of the id property.
setID(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK: Sets the value of the id property.
setIdentitySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field identitySamples.
setILLUMINA(ExperimentType.PLATFORM.ILLUMINA) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Sets the value of the illumina property.
setIncludeCoverage(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field includeCoverage.
setIncludeCoverage(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field includeCoverage.
setIncludeIndels(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field includeIndels.
setIncludeIndels(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field includeIndels.
setIncludeIndels(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field includeIndels.
setIncludeSNV(boolean) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field includeSNV.
setIncludeSNV(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field includeSNV.
setIncludeSNVs(boolean) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field includeSNVs.
setIndividualName(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field individualName.
setInfo(String) - Method in class net.sourceforge.solexatools.util.PageInfo: Setter for the field info.
setInformOnError(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT: Sets the value of the informOnError property.
setInformOnStatus(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT: Sets the value of the informOnStatus property.
setIniFile(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field iniFile.
setInput(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field input.
setInput(String) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field input.
setInputAlgorithm(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field inputAlgorithm.
setInputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field inputFiles.
setInstalled(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
setInstitution(String) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field institution.
setInstitution(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Setter for the field institution.
setInstrumentModel(String) - Method in class net.sourceforge.seqware.common.model.Platform: Setter for the field instrumentModel.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID: Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.HELICOS: Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ILLUMINA: Sets the value of the instrumentmodel property.
setINSTRUMENTMODEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.LS454: Sets the value of the instrumentmodel property.
setInstrumentModel(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the instrumentModel property.
setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field instrumentName.
setInstrumentName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field instrumentName.
setInstrumentName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the instrumentName property.
setInvitationCode(String) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field invitationCode.
setInvoice(Invoice) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field invoice.
setInvoiceDAO(InvoiceDAO) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: setInvoiceDAO.
setInvoiceDAO(InvoiceDAO) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: setInvoiceDAO.
setInvoiceId(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field invoiceId.
setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.InvoiceDetailsController: Setter for the field invoiceService.
setInvoiceService(InvoiceService) - Method in class net.sourceforge.solexatools.webapp.controller.OpenInvoiceController: Setter for the field invoiceService.
setIsEnd(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo: Setter for the field isEnd.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field isHasFile.
setIsHasFile(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field isHasFile.
setIsInput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile: isInput = @param isInput isOutput = !@param isInput
setIsOutput(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile: isInput = !@param isOutput isOutput = @param isOutput
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field isSelected.
setIsSelected(Boolean) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field isSelected.
setIsStart(boolean) - Method in class net.sourceforge.solexatools.util.PageInfo: Setter for the field isStart.
setItemRgb(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field itemRgb.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSAttribute: Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.IUSLink: Setter for the field ius.
setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Lane: setIUS.
setIUS(Set<IUS>) - Method in class net.sourceforge.seqware.common.model.Processing: setIUS.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Setter for the field ius.
setIUS(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.Sample: setIUS.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Setter for the field ius.
setIus(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field ius.
setIus(IUS) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Setter for the field ius.
setIusAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.IUSAttribute: Setter for the field iusAttributeId.
setIusAttributes(Set<IUSAttribute>) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field iusAttributes.
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: setIUSDAO.
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: setIUSDAO.
setIUSDAO(IUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: Sets a private member variable with an instance of an implementation of IUSDAO.
setIUSDAO(IUSDAO) - Method in interface net.sourceforge.seqware.common.business.IUSService: setIUSDAO.
setIusId(Integer) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field iusId.
setIusLinkId(int) - Method in class net.sourceforge.seqware.common.model.IUSLink: Setter for the field iusLinkId.
setIusLinks(Set<IUSLink>) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field iusLinks.
setIusService(IUSService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field iusService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: setIUSService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.IUSSetupController: Setter for the field iusService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: setIUSService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: setIUSService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: setIUSService.
setIusService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field iusService.
setIUSService(IUSService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: setIUSService.
setIusSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setJdbcTemplate(SimpleJdbcTemplate) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect: Setter for the field jdbcTemplate.
setJoinDevelopersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field joinDevelopersMailingList.
setJoinUsersMailingList(boolean) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field joinUsersMailingList.
setKey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setKey(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder: ' Should not be called outside of the back-end
setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field key.
setKey(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Setter for the field key.
setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument: Setter for the field key.
setKey(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile: Setter for the field key.
setKeyIndex(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field keyIndex.
setKeyvalues(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model: Setter for the field keyvalues.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.IUSLink: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.LaneLink: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.SampleLink: Setter for the field label.
setLabel(String) - Method in class net.sourceforge.seqware.common.model.StudyLink: Setter for the field label.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK: Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK: Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK: Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK: Sets the value of the label property.
setLABEL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK: Sets the value of the label property.
setLabName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the labName property.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.LaneLink: Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Setter for the field lane.
setLane(Lane) - Method in class net.sourceforge.seqware.common.model.ShareLane: Setter for the field lane.
setLane(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setLane1(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane1.
setLane2(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane2.
setLane3(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane3.
setLane4(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane4.
setLane5(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane5.
setLane6(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane6.
setLane7(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane7.
setLane8(Lane) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lane8.
setLane_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field lane_url.
setLaneAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Setter for the field laneAttributeId.
setLaneAttributes(Set<LaneAttribute>) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field laneAttributes.
setLaneCount(int) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO: Setter for the field laneCount.
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Setter for the field laneDAO.
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: setLaneDAO.
setLaneDAO(LaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: Sets a private member variable with an instance of an implementation of LaneDAO.
setLaneDAO(LaneDAO) - Method in interface net.sourceforge.seqware.common.business.LaneService: setLaneDAO.
setLaneForSequrncerRun(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setLaneForSequrncerRun.
setLaneForStudy(Lane, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setLaneForStudy.
setLaneId(Integer) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field laneId.
setLaneIndex(Integer) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field laneIndex.
setLaneLinkId(int) - Method in class net.sourceforge.seqware.common.model.LaneLink: Setter for the field laneLinkId.
setLaneLinks(Set<LaneLink>) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field laneLinks.
setLanes(Set<Lane>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field lanes.
setLanes(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field lanes.
setLaneService(LaneService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.validation.LaneValidator: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSetupController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field laneService.
setLaneService(LaneService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Setter for the field laneService.
setLanesForView(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.model.Sample: setLanesForView.
setLaneString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setLaneSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setLastName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setLastName(String) - Method in class com.github.seqware.queryengine.model.User.Builder
setLastName(String) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field lastName.
setLastName(String) - Method in class net.sourceforge.seqware.webservice.dto.OwnerDto: Setter for the field lastName.
setLatestDate(Date) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport: Set the value of latestDate.
setLayout(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field layout.
setLeastSigBits(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
setLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field length.
setLIBRARYCONSTRUCTIONPROTOCOL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Sets the value of the libraryconstructionprotocol property.
setLIBRARYDESCRIPTOR(ExperimentType.DESIGN.LIBRARYDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Sets the value of the librarydescriptor property.
setLibraryId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto: Setter for the field libraryId.
setLIBRARYLAYOUT(ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Sets the value of the librarylayout property.
setLIBRARYNAME(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Sets the value of the libraryname property.
setLibrarySamples(Collection<Sample>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field librarySamples.
setLibrarySelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.Lane
setLIBRARYSELECTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Sets the value of the libraryselection property.
setLibrarySelectionDAO(LibrarySelectionDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl: setLibrarySelectionDAO.
setLibrarySelectionDAO(LibrarySelectionDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService: setLibrarySelectionDAO.
setLibrarySelectionId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySelection: Setter for the field librarySelectionId.
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.seqware.common.ContextImpl
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field librarySelectionService.
setLibrarySelectionService(LibrarySelectionService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Setter for the field librarySelectionService.
setLibraryService(LibraryService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field libraryService.
setLibrarySource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.Lane
setLIBRARYSOURCE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Sets the value of the librarysource property.
setLibrarySourceDAO(LibrarySourceDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl: setLibrarySourceDAO.
setLibrarySourceDAO(LibrarySourceDAO) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService: setLibrarySourceDAO.
setLibrarySourceId(Integer) - Method in class net.sourceforge.seqware.common.model.LibrarySource: Setter for the field librarySourceId.
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.seqware.common.ContextImpl
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field librarySourceService.
setLibrarySourceService(LibrarySourceService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Setter for the field librarySourceService.
setLibraryStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.Lane
setLIBRARYSTRATEGY(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR: Sets the value of the librarystrategy property.
setLibraryStrategyDAO(LibraryStrategyDAO) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl: setLibraryStrategyDAO.
setLibraryStrategyDAO(LibraryStrategyDAO) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService: setLibraryStrategyDAO.
setLibraryStrategyId(Integer) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy: Setter for the field libraryStrategyId.
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.seqware.common.ContextImpl
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field libraryStrategyService.
setLibraryStrategyService(LibraryStrategyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Setter for the field libraryStrategyService.
setLibraryType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Setter for the field libraryType.
setLIMSAdmin(boolean) - Method in class net.sourceforge.seqware.common.model.Registration: setLIMSAdmin.
setList(List<Experiment>) - Method in class net.sourceforge.seqware.common.model.lists.ExperimentList: setList.
setList(List<File>) - Method in class net.sourceforge.seqware.common.model.lists.FileList: setList.
setList(List<IUS>) - Method in class net.sourceforge.seqware.common.model.lists.IUSList: setList.
setList(List<Lane>) - Method in class net.sourceforge.seqware.common.model.lists.LaneList: setList.
setList(List<LibrarySelection>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList: setList.
setList(List<LibrarySource>) - Method in class net.sourceforge.seqware.common.model.lists.LibrarySourceList: setList.
setList(List<LibraryStrategy>) - Method in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList: setList.
setList(List<Organism>) - Method in class net.sourceforge.seqware.common.model.lists.OrganismList: setList.
setList(List<Platform>) - Method in class net.sourceforge.seqware.common.model.lists.PlatformList: setList.
setList(List<Processing>) - Method in class net.sourceforge.seqware.common.model.lists.ProcessingList: setList.
setList(List<ReturnValue>) - Method in class net.sourceforge.seqware.common.model.lists.ReturnValueList: setList.
setList(List<Sample>) - Method in class net.sourceforge.seqware.common.model.lists.SampleList: setList.
setList(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.lists.SequencerRunList: setList.
setList(List<Study>) - Method in class net.sourceforge.seqware.common.model.lists.StudyList: setList.
setList(List<StudyType>) - Method in class net.sourceforge.seqware.common.model.lists.StudyTypeList: setList.
setList(List<Workflow>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowList: setList.
setList(List<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamList: setList.
setList(List<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList: setList.
setList(Collection<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList: setList.
setList(List<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2: setList.
setLS454(ExperimentType.PLATFORM.LS454) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM: Sets the value of the ls454 property.
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Analysis.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Group.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Set the model manager for this Atom
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.impl.FeatureList.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.interfaces.BaseBuilder: Set a manager for this Atom
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Reference.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.Tag.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
setManager(CreateUpdateManager) - Method in class com.github.seqware.queryengine.model.User.Builder
setMaxCoverage(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field maxCoverage.
setMaxCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field maxCoverage.
setMaxCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field maxCoverage.
setMaximumMappingQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field maximumMappingQuality.
setMaximumMappingQuality(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field maximumMappingQuality.
setMaxLockers(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field maxLockers.
setMaxLockObjects(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field maxLockObjects.
setMaxLocks(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field maxLocks.
setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
setMaxMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
setMaxMemory(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: set max memory
setMd5sum(String) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field md5sum.
setMd5sum(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setMd5sum(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setMd5sum(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Setter for the field md5sum.
setMEMBERS(SampleType.MEMBERS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Sets the value of the members property.
setMemory(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
setMemReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field memReq.
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: Setter for the field metadata.
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.decider.Decider: Lets you set the metadata object
setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Lets you set the metadata object
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.module.Module: Setter for the field metadata.
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: Lets you set the metadata object
setMetadata(Metadata) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Lets you set the metadata object
setMetadata(Metadata) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Lets you set the metadata object
setMetadata_output_dir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
setMetadata_output_file_prefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set output file prefix, used by provisionfiles output
setMetadataOutputPrefix(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
setMetadataWriteback(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setMetadataWriteBack(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: need metadata writeback? user can override this setting by using --no-metadata or --metadata from command line
setMetadataWriteback(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
setMetaType(String) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field metaType.
setMetaType(String) - Method in class net.sourceforge.seqware.common.model.FileType: Setter for the field metaType.
setMetaType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setMetaType(List<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setMetaType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Setter for the field metaType.
setMimeType(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setMinCoverage(int) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field minCoverage.
setMinCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field minCoverage.
setMinCoverage(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field minCoverage.
setMinObservations(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field minObservations.
setMinObservationsPerStrand(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field minObservationsPerStrand.
setMinPercent(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field minPercent.
setMinSnpQuality(float) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field minSnpQuality.
setMinSnpQuality(float) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field minSnpQuality.
setMinSNVPhred(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field minSNVPhred.
setMismatchAAChangeBlosumScore(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchAAChangeBlosumScore.
setMismatchAminoAcidChange(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchAminoAcidChange.
setMismatchChr(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchChr.
setMismatchCodonChange(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchCodonChange.
setMismatchCodonPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchCodonPosition.
setMismatchId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchId.
setMismatchStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchStart.
setMismatchStop(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchStop.
setMismatchType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mismatchType.
setMODIFY(SubmissionType.ACTIONS.ACTION.MODIFY) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Sets the value of the modify property.
setModuleParameter(List<String>) - Method in class net.sourceforge.seqware.pipeline.runner.Runner2: Setter for the field moduleParameter.
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setMol(QueryEngine.MoleculePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setMol(QueryEngine.MoleculePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setMostSigBits(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
setMULTIPLIER(double) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Sets the value of the multiplier property.
setMutatedGenomicSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mutatedGenomicSequence.
setMutatedTranslatedSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field mutatedTranslatedSequence.
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setName(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.AnalysisSet.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.Group.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.Reference.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
setName(String) - Method in class com.github.seqware.queryengine.model.TagSet.Builder
setName(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySelection: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.LibrarySource: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.LibraryStrategy: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Organism: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Platform: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.StudyType: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set the workflow name
setName(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
setName(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the name property.
setName(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT: Sets the value of the name property.
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field name.
setName(String) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto: Setter for the field name.
setName(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
setNameNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field nameNode.
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile: setNamespace.
setNamespace(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
setNcbiTaxId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism: Setter for the field ncbiTaxId.
setNcbiTaxonomyId(Integer) - Method in class net.sourceforge.seqware.webservice.dto.OrganismDto: Setter for the field ncbiTaxonomyId.
setNetwork(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
setNetworkReq(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field networkReq.
setNewStudyType(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE: Sets the value of the newStudyType property.
setNewType(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field newType.
SetNodeIdInSession - Class in net.sourceforge.solexatools.util: SetNodeIdInSession class.
SetNodeIdInSession() - Constructor for class net.sourceforge.solexatools.util.SetNodeIdInSession
setNominalLength(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field nominalLength.
setNOMINALLENGTH(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED: Sets the value of the nominallength property.
setNominalSdev(Long) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field nominalSdev.
setNOMINALSDEV(Double) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED: Sets the value of the nominalsdev property.
setNotes(String) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field notes.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD: Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY: Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE: Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS: Sets the value of the notes property.
setNotes(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE: Sets the value of the notes property.
setNotRunned(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field notRunned.
setNumberChannels(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the numberChannels property.
setNUMBEROFLEVELS(int) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Sets the value of the numberoflevels property.
setNUMBEROFREADSPERSPOT(long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC: Sets the value of the numberofreadsperspot property.
setOffspringProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field offspringProcessings.
setOrganism(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setOrganism(String) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet.Builder
setOrganism(String) - Method in class com.github.seqware.queryengine.model.ReferenceSet.Builder
setOrganism(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field organism.
setOrganism(Organism) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field organism.
setOrganism(OrganismDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field organism.
setOrganismDAO(OrganismDAO) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl: setOrganismDAO.
setOrganismDAO(OrganismDAO) - Method in interface net.sourceforge.seqware.common.business.OrganismService: setOrganismDAO.
setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Organism: Setter for the field organismId.
setOrganismId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field organismId.
setOrganismService(OrganismService) - Method in class net.sourceforge.seqware.common.ContextImpl
setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Setter for the field organismService.
setOrganismService(OrganismService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Setter for the field organismService.
setORIENTATION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED: Sets the value of the orientation property.
setOriginalFileName(String) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Setter for the field originalFileName.
setOs(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: Setter for the field outputDir.
setOutputDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.ProvisionFilesJob
setOutputFilename(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Setter for the field outputFilename.
setOutputFilename(String) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field outputFilename.
setOutputFiles(Collection<File>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field outputFiles.
setOwner(SGID) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder: Set the SGID for the owner permissions
setOwner(User) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder: Set the user permissions
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field owner.
setOwner(Registration) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field owner.
setOwner(OwnerDto) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field owner.
setOwnerId(Integer) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field ownerId.
setPage(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Setter for the field page.
setPaidAmount(Double) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field paidAmount.
setPAIRED(ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT.PAIRED) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT: Sets the value of the paired property.
setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field pairedEnd.
setPairedEnd(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field pairedEnd.
setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field pairedFilePath.
setPairedFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field pairedFilePath.
setPairedOrientation(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field pairedOrientation.
setParameter(RPNStack.Parameter, Object) - Method in class com.github.seqware.queryengine.kernel.RPNStack: Sets a parameter to a concrete value.
setParameters(ByteString) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
setParameters(List<Object>) - Method in class com.github.seqware.queryengine.model.Analysis.Builder: Set the group for the current Atom
setParameters(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field parameters.
setParameters(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field parameters.
setParameters(List<String>) - Method in class net.sourceforge.seqware.pipeline.module.Module: setParameters.
setParameters(List<String>) - Method in interface net.sourceforge.seqware.pipeline.module.ModuleInterface: setParameters.
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.decider.Decider: Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.decider.DeciderInterface: Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugin.Plugin: Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in interface net.sourceforge.seqware.pipeline.plugin.PluginInterface: Lets you set a List of params so the plugin can deal with parameters
setParams(List<String>) - Method in class net.sourceforge.seqware.pipeline.plugins.HelloWorld: Lets you set a List of params so the plugin can deal with parameters
setParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryLine: Setter for the field params.
setPARENT(AnalysisType.PARENT) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the parent property.
setParent_accessions(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
setParentAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
setParentProcessingAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Setter for the field parentProcessingAccession.
setParentProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field parentProcessings.
setParents(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field parents.
setParents(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field parents.
setParents(Collection<Job>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob: set parent jobs
setParentUrls(Set<String>) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field parentUrls.
setParentWorkflowAccessions(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setPassword(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setPassword(String) - Method in class com.github.seqware.queryengine.model.User.Builder
setPassword(String) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field password.
setPassword(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field password.
setPasswordHint(String) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field passwordHint.
setPasswordWithoutHash(String) - Method in class com.github.seqware.queryengine.model.User.Builder
setPathToFirstFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field pathToFirstFile.
setPathToSecondFile(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field pathToSecondFile.
setPayee(boolean) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field payee.
setPeakMemory(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment: set the max memory for the workflow
setPeakThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment: set the max threads for the workflow
setPegasusConfigDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
setPending(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field pending.
setPermanentBundleLocation(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field permanentBundleLocation.
setPermBundleLocation(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field permBundleLocation.
setPermissions(ACL) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Set permissions for this
setPermissions(ACL) - Method in interface com.github.seqware.queryengine.model.interfaces.ACLable: Set permissions for this
setPfn(Pfn) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
setPhase(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setPhase(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field platform.
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field platform.
setPlatform(Platform) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field platform.
setPLATFORM(ExperimentType.PLATFORM) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the platform property.
setPlatformDAO(PlatformDAO) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl: setPlatformDAO.
setPlatformDAO(PlatformDAO) - Method in interface net.sourceforge.seqware.common.business.PlatformService: setPlatformDAO.
setPlatformId(Integer) - Method in class net.sourceforge.seqware.common.model.Platform: Setter for the field platformId.
setPlatformInt(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field platformInt.
setPlatformInt(int) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field platformInt.
setPlatformService(PlatformService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Setter for the field platformService.
setPlatformService(PlatformService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController: Setter for the field platformService.
setPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.model.Analysis.Builder
setPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.model.Analysis: Set up the analysis plug-in
setPlugin(AnalysisPluginInterface) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Set up the analysis plug-in
setPmi(Importer) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field pmi.
setPmi(Importer) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field pmi.
setPostgresqlPersistenceStrategy(int) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field postgresqlPersistenceStrategy.
setPragma(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setPragma(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setPrecedingID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setPrecedingID(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setPrecedingID(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setPrecedingID(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setPrecedingSGID(SGID) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Used in back-end to set previous version without side-effects
setPrecedingVersion(QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setPrecedingVersion(QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setPrecedingVersion(QueryEngine.AnalysisPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
setPrecedingVersion(QueryEngine.AnalysisPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB.Builder
setPrecedingVersion(QueryEngine.AnalysisSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setPrecedingVersion(QueryEngine.AnalysisSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB.Builder
setPrecedingVersion(QueryEngine.FeaturePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setPrecedingVersion(QueryEngine.FeaturePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setPrecedingVersion(QueryEngine.FeatureSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setPrecedingVersion(QueryEngine.FeatureSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setPrecedingVersion(QueryEngine.GroupPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setPrecedingVersion(QueryEngine.GroupPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setPrecedingVersion(QueryEngine.ReferencePB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setPrecedingVersion(QueryEngine.ReferencePB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB.Builder
setPrecedingVersion(QueryEngine.ReferenceSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setPrecedingVersion(QueryEngine.ReferenceSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setPrecedingVersion(QueryEngine.TagSetPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setPrecedingVersion(QueryEngine.TagSetPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setPrecedingVersion(QueryEngine.UserPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setPrecedingVersion(QueryEngine.UserPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB.Builder
setPrecedingVersion(T) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Explicitly set the previous version of a Atom.
setPrecedingVersion(T) - Method in interface com.github.seqware.queryengine.model.interfaces.Versionable: Explicitly set the previous version of a Atom.
setPredicate(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setPredicate(String) - Method in class com.github.seqware.queryengine.model.Tag.Builder
setPricePerUnit(Double) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field pricePerUnit.
setPrivate(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow: setPrivate.
setProcCountInfo(List<SequencerRun>) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: setProcCountInfo.
setProcCountInfo(List<SequencerRun>) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: setProcCountInfo.
setProcess(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field process.
setProcessedCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field processedCount.
setProcessExitStatus(Integer) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field processExitStatus.
setProcessExitStatus(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field processExitStatus.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Setter for the field processing.
setProcessing(Processing) - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Setter for the field processing.
setPROCESSING(ExperimentType.PROCESSING) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the processing property.
setProcessingAccession(int) - Method in class net.sourceforge.seqware.pipeline.module.Module: Setter for the field processingAccession.
setProcessingAttributeId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: Setter for the field processingAttributeId.
setProcessingAttributes(Set<ProcessingAttribute>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field processingAttributes.
setProcessingByChildId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Setter for the field processingByChildId.
setProcessingByParentId(Processing) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Setter for the field processingByParentId.
setProcessingCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field processingCount.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Setter for the field processingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: Sets a private member variable with an instance of an implementation of ProcessingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: setProcessingDAO.
setProcessingDAO(ProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: Setter for the field processingDAO.
setProcessingDAO(ProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: setProcessingDAO.
setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl: setProcessingExperimentsDAO.
setProcessingExperimentsDAO(ProcessingExperimentsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService: setProcessingExperimentsDAO.
setProcessingExperimentsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Setter for the field processingExperimentsId.
setProcessingExperimentsService(ProcessingExperimentsService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingExperimentsService.
setProcessingForSequrncerRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setProcessingForSequrncerRun.
setProcessingForStudy(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setProcessingForStudy.
setProcessingForWorkflowRun(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setProcessingForWorkflowRun.
setProcessingForWorkflowRunRunning(Processing, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setProcessingForWorkflowRunRunning.
setProcessingId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field processingId.
setProcessingIUSDAO(ProcessingIUSDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl: setProcessingIUSDAO.
setProcessingIUSDAO(ProcessingIUSDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService: setProcessingIUSDAO.
setProcessingIusId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Setter for the field processingIusId.
setProcessingIusService(ProcessingIUSService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingIusService.
setProcessingLanesDAO(ProcessingLanesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl: setProcessingLanesDAO.
setProcessingLanesDAO(ProcessingLanesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService: setProcessingLanesDAO.
setProcessingLaneService(ProcessingLanesService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingLaneService.
setProcessingLanesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Setter for the field processingLanesId.
setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl: setProcessingRelationshipDAO.
setProcessingRelationshipDAO(ProcessingRelationshipDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService: setProcessingRelationshipDAO.
setProcessingRelationshipId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Setter for the field processingRelationshipId.
setProcessingRelationshipService(ProcessingRelationshipService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingRelationshipService.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field processings.
setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field processings.
setProcessings(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field processings.
setProcessings(SortedSet<Processing>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field processings.
setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl: setProcessingSamplesDAO.
setProcessingSamplesDAO(ProcessingSamplesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService: setProcessingSamplesDAO.
setProcessingSamplesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Setter for the field processingSamplesId.
setProcessingSamplesService(ProcessingSamplesService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingSamplesService.
setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl: setProcessingSequencerRunsDAO.
setProcessingSequencerRunsDAO(ProcessingSequencerRunsDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService: setProcessingSequencerRunsDAO.
setProcessingSequencerRunService(ProcessingSequencerRunsService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingSequencerRunService.
setProcessingSequencerRunsId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Setter for the field processingSequencerRunsId.
setProcessingService(ProcessingService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field processingService.
setProcessingService(ProcessingService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Setter for the field processingService.
setProcessingsForView(Set<Processing>) - Method in class net.sourceforge.seqware.common.model.Lane: setProcessingsForView.
setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl: setProcessingStudiesDAO.
setProcessingStudiesDAO(ProcessingStudiesDAO) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService: setProcessingStudiesDAO.
setProcessingStudiesId(int) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Setter for the field processingStudiesId.
setProcessingStudiesService(ProcessingStudiesService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field processingStudiesService.
setProjectDAO(ProjectDAO) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: setProjectDAO.
setProjectDAO(ProjectDAO) - Method in interface net.sourceforge.seqware.common.business.ProjectService: setProjectDAO.
setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field projectId.
setProjectId(Integer) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field projectId.
setPROJECTID(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Sets the value of the projectid property.
setPROTECT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Sets the value of the protect property.
setPublic(boolean) - Method in class net.sourceforge.seqware.common.model.Workflow: setPublic.
setQCREPORT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the qcreport property.
setQtype(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Sets the value of the qtype property.
setQualityMultiplier(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field qualityMultiplier.
setQualityNumberOfLevels(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field qualityNumberOfLevels.
setQualityScorer(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field qualityScorer.
setQUALITYSCORER(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.QUALITYSCORES: Sets the value of the qualityscorer property.
setQualityType(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field qualityType.
setQueue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
setQueue(String) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: set the queue
setRandom(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set the pre-defined random variable
setReadBases(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field readBases.
setReadClass(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field readClass.
setREADCLASS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Sets the value of the readclass property.
setReadCount(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field readCount.
setReader(BufferedReader) - Method in class net.sourceforge.seqware.common.util.iotools.BufferedReaderThread: Setter for the field reader.
setReadIndex(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field readIndex.
setREADINDEX(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Sets the value of the readindex property.
setReadLabel(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field readLabel.
setReadOnly(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field readOnly.
setReadSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Setter for the field readSpec.
setReadSpecs(SortedSet<ExperimentSpotDesignReadSpec>) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Setter for the field readSpecs.
setReadsPerSpot(Integer) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Setter for the field readsPerSpot.
setReadsSupportingCallOne(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field readsSupportingCallOne.
setReadsSupportingCallThree(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field readsSupportingCallThree.
setReadsSupportingCallTwo(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field readsSupportingCallTwo.
setReadType(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec: Setter for the field readType.
setREADTYPE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC.READSPEC: Sets the value of the readtype property.
setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: setReadyToProcess.
setReadyToProcess(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field readyToProcess.
setReference(Reference) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
setReference(Reference) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
setReference(Reference) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
setReferenceACL(ACL, Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setReferenceACL.
setREFERENCEALIGNMENT(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the referencealignment property.
setReferenceAveSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field referenceAveSeqQuality.
setReferenceBase(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field referenceBase.
setReferenceCallQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field referenceCallQuality.
setReferenceID(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setReferenceID(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB.Builder
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.FeatureSet.Builder
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet.Builder
setReferenceID(SGID) - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet.Builder
setReferenceId(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field referenceId.
setReferenceIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setReferenceIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB.Builder
setReferenceMaxSeqQuality(float) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field referenceMaxSeqQuality.
setReferenceSetACL(ACL, ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setReferenceSetACL.
setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field refLane.
setRefLane(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field refLane.
setRefName(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.EXPERIMENTREF: Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.RUNREF: Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEREF: Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.STUDYREF: Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SAMPLEDESCRIPTOR: Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.STUDYREF: Sets the value of the refname property.
setRefname(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.EXPERIMENTREF: Sets the value of the refname property.
setRegion(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the region property.
setRegions(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field regions.
setRegions(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field regions.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareFile: Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareLane: Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareSample: Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareStudy: Setter for the field registration.
setRegistration(Registration) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Setter for the field registration.
setRegistrationDAO(RegistrationDAO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: setRegistrationDAO.
setRegistrationDAO(RegistrationDAO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: setRegistrationDAO.
setRegistrationId(Integer) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field registrationId.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Static method in class net.sourceforge.seqware.webservice.resources.BasicResource: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserValidatorController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.LoginController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationSetupController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.SignUpController: Setter for the field registrationService.
setRegistrationService(RegistrationService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Setter for the field registrationService.
setRelationship(String) - Method in class net.sourceforge.seqware.common.model.ProcessingRelationship: Setter for the field relationship.
setRelativeLocation(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field relativeLocation.
setRELEASE(SubmissionType.ACTIONS.ACTION.RELEASE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Sets the value of the release property.
setRequireFiles(boolean) - Method in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Setter for the field requireFiles.
setRequirements(Collection<Requirement>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
setReturnIds(boolean) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field returnIds.
setReturnValue(ReturnValue) - Method in exception net.sourceforge.seqware.common.err.OldSeqwareException: Setter for the field returnValue.
setReturnValue(int) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field returnValue.
setRights(int, boolean) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
setRights(boolean[]) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
setRights(List<Boolean>) - Method in class com.github.seqware.queryengine.model.interfaces.ACL.Builder
setRootProcessingName(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setRootProcessingSwa(String) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setRootSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Setter for the field rootSample.
setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field rowId.
setRowId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field rowId.
setRowKey(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
setRows(List<Flexigrid.Cells>) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Setter for the field rows.
setRUNATTRIBUTES(RunType.RUNATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the runattributes property.
setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field runCenter.
setRunCenter(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field runCenter.
setRunCenter(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the runCenter property.
setRunDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the runDate property.
setRunFile(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the runFile property.
setRUNLINKS(RunType.RUNLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the runlinks property.
setRUNREF(AnalysisType.PARENT.RUNREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Sets the value of the runref property.
setRunStartTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field runStartTimestamp.
setRunStartTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field runStartTstmp.
setRunStopTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field runStopTimestamp.
setRunStopTstmp(Date) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field runStopTstmp.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleAttribute: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleLink: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.SampleSearch: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.ShareSample: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field sample.
setSample(Sample) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field sample.
setSample(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setSample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field sample.
setSample_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field sample_url.
setSampleAttributeId(int) - Method in class net.sourceforge.seqware.common.model.SampleAttribute: Setter for the field sampleAttributeId.
setSampleAttributes(Set<SampleAttribute>) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field sampleAttributes.
setSAMPLEATTRIBUTES(SampleType.SAMPLEATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Sets the value of the sampleattributes property.
setSampleCode(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field sampleCode.
setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Setter for the field sampleDAO.
setSampleDAO(SampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: setSampleDAO.
setSampleDAO(SampleDAO) - Method in interface net.sourceforge.seqware.common.business.SampleService: setSampleDAO.
setSAMPLEDESCRIPTOR(ExperimentType.DESIGN.SAMPLEDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Sets the value of the sampledescriptor property.
setSampleForStudy(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setSampleForStudy.
setSampleForWorkflowRun(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setSampleForWorkflowRun.
setSampleForWorkflowRunRunning(Sample, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setSampleForWorkflowRunRunning.
setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field sampleId.
setSampleId(Integer) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field sampleId.
setSampleId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER: Sets the value of the sampleId property.
setSampleId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER: Sets the value of the sampleId property.
setSampleId(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryIdentityDto: Setter for the field sampleId.
setSampleLinkId(int) - Method in class net.sourceforge.seqware.common.model.SampleLink: Setter for the field sampleLinkId.
setSampleLinks(Set<SampleLink>) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field sampleLinks.
setSAMPLELINKS(SampleType.SAMPLELINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Sets the value of the samplelinks property.
setSAMPLENAME(SampleType.SAMPLENAME) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType: Sets the value of the samplename property.
setSAMPLEPOOLREF(AnalysisType.PARENT.SAMPLEPOOLREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Sets the value of the samplepoolref property.
setSampleRef(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT.SAMPLEPOOLREF.MEMBER: Sets the value of the sampleRef property.
setSAMPLEREF(AnalysisType.PARENT.SAMPLEREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Sets the value of the sampleref property.
setSampleRef(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.MEMBERS.MEMBER: Sets the value of the sampleRef property.
setSampleReportDAO(SampleReportDAO) - Method in class net.sourceforge.seqware.common.business.impl.SampleReportServiceImpl: Setter for the field sampleReportDAO.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field sampleReportService.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Setter for the field sampleReportService.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Setter for the field sampleReportService.
setSampleReportService(SampleReportService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Setter for the field sampleReportService.
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field samples.
setSamples(Set<Sample>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field samples.
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field samples.
setSamples(SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field samples.
setSampleSearch(SampleSearch) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: Setter for the field sampleSearch.
setSampleSearchAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: Setter for the field sampleSearchAttributeId.
setSampleSearchAttributes(Set<SampleSearchAttribute>) - Method in class net.sourceforge.seqware.common.model.SampleSearch: Setter for the field sampleSearchAttributes.
setSampleSearchId(Integer) - Method in class net.sourceforge.seqware.common.model.SampleSearch: Setter for the field sampleSearchId.
setSampleService(SampleService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.validation.SampleValidator: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaneSampleAssociateSetupController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleSetupController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SaveOpenNodeController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Setter for the field sampleService.
setSampleService(SampleService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController: Setter for the field sampleService.
setSampleSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setSampleType(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field sampleType.
setSampleUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto: Setter for the field sampleUrl.
setSchema(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD: Sets the value of the schema property.
setSchema(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE: Sets the value of the schema property.
setScore(double) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setScore(Double) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setScore(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field score.
setSector(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the sector property.
setSelection(LibrarySelection) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field selection.
setSender(MailSender) - Method in class net.sourceforge.solexatools.webapp.controller.InviteNewUserController: Setter for the field sender.
setSeqid(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setSequencer_run_url(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field sequencer_run_url.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field sequencerRun.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Setter for the field sequencerRun.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field sequencerRun.
setSequencerRun(SequencerRun) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Setter for the field sequencerRun.
setSequencerRun(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setSequencerRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setSequencerRun.
setSequencerRunAttributeId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: Setter for the field sequencerRunAttributeId.
setSequencerRunAttributes(Set<SequencerRunAttribute>) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field sequencerRunAttributes.
setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Setter for the field sequencerRunDAO.
setSequencerRunDAO(SequencerRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: setSequencerRunDAO.
setSequencerRunDAO(SequencerRunDAO) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: setSequencerRunDAO.
setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field sequencerRunId.
setSequencerRunId(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field sequencerRunId.
setSequencerRuns(Set<SequencerRun>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field sequencerRuns.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingSetupController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunListDetailsController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportSetupController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunSetupControllerDTO: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardSetupController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field sequencerRunService.
setSequencerRunService(SequencerRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Setter for the field sequencerRunService.
setSequencerRunSwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setSequencerRunValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Setter for the field sequencerRunValidator.
setSequencerRunWizardDTO(SequencerRunWizardDTO) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: setSequencerRunWizardDTO.
setSequencerRunWizardValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunWizardController: Setter for the field sequencerRunWizardValidator.
setSequenceSpace(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field sequenceSpace.
setSEQUENCESPACE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PROCESSING.BASECALLS: Sets the value of the sequencespace property.
setSEQUENCINGPROTOCOL(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the sequencingprotocol property.
setSeqwareAccession(Integer) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setSeqwareAccessionString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setSeqwareRevision(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field seqwareRevision.
setSeqwareVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field seqwareVersion.
setSerializationConstant(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setSerializationConstant(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setServer(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field server.
setSessionFactory(SessionFactory) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field sessionFactory.
setSettings(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setSettings.
setSettings(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: setSettings.
setSettings(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: setSettings.
setSettings(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: setSettings.
setSETTINGS_MAP(Map<String, String>) - Static method in class com.github.seqware.queryengine.Constants: Set the settings map, overriding hard-coded values for our constants.
setSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setSgid(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setSgid(QESupporting.FSGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setSgid(QESupporting.FSGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setSgid(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
setSgid(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
setSGID(SGID) - Method in class com.github.seqware.queryengine.util.LazyReference: Set the SGID of the object to be lazy referenced
setSharedStudies(SortedSet<ShareStudy>) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field sharedStudies.
setSharedWorkflowRuns(SortedSet<ShareWorkflowRun>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field sharedWorkflowRuns.
setShareExperimentDAO(ShareExperimentDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: setShareExperimentDAO.
setShareExperimentDAO(ShareExperimentDAO) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: setShareExperimentDAO.
setShareExperimentId(int) - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Setter for the field shareExperimentId.
setShareFileDAO(ShareFileDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: setShareFileDAO.
setShareFileDAO(ShareFileDAO) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: setShareFileDAO.
setShareFileId(int) - Method in class net.sourceforge.seqware.common.model.ShareFile: Setter for the field shareFileId.
setShareLaneDAO(ShareLaneDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: setShareLaneDAO.
setShareLaneDAO(ShareLaneDAO) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: setShareLaneDAO.
setShareLaneId(int) - Method in class net.sourceforge.seqware.common.model.ShareLane: Setter for the field shareLaneId.
setShareProcessingDAO(ShareProcessingDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: setShareProcessingDAO.
setShareProcessingDAO(ShareProcessingDAO) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: setShareProcessingDAO.
setShareProcessingId(int) - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Setter for the field shareProcessingId.
setShareSampleDAO(ShareSampleDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: setShareSampleDAO.
setShareSampleDAO(ShareSampleDAO) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: setShareSampleDAO.
setShareSampleId(int) - Method in class net.sourceforge.seqware.common.model.ShareSample: Setter for the field shareSampleId.
setShareStudyDAO(ShareStudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: setShareStudyDAO.
setShareStudyDAO(ShareStudyDAO) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: setShareStudyDAO.
setShareStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy: Setter for the field shareStudyId.
setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Setter for the field shareStudyService.
setShareStudyService(ShareStudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Setter for the field shareStudyService.
setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: setShareWorkflowRunDAO.
setShareWorkflowRunDAO(ShareWorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: setShareWorkflowRunDAO.
setShareWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Setter for the field shareWorkflowRunId.
setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Setter for the field shareWorkflowRunService.
setShareWorkflowRunService(ShareWorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Setter for the field shareWorkflowRunService.
setSINGLE(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT: Sets the value of the single property.
setSite(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn: Setter for the field site.
setSize(Long) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field size.
setSize(Long) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setSize(Long) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setSize(Long) - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Setter for the field size.
setSizeString(String) - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field skip.
setSkip(Boolean) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field skip.
setSkipTxt(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field skipTxt.
setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field slideOneFilePath.
setSlideOneFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field slideOneFilePath.
setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field slideOneLaneCount.
setSlideOneLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field slideOneLaneCount.
setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field slideTwoFilePath.
setSlideTwoFilePath(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field slideTwoFilePath.
setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field slideTwoLaneCount.
setSlideTwoLaneCount(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field slideTwoLaneCount.
setSortable(boolean) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
setSortKeySample(Sample) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field sortKeySample.
setSource(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setSource(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setSource(LibrarySource) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field source.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field source.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD: Sets the value of the source property.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY: Sets the value of the source property.
setSource(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE: Sets the value of the source property.
setSourcePath(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
setSPOTDECODEMETHOD(Long) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR: Sets the value of the spotdecodemethod property.
setSPOTDECODESPEC(ExperimentType.DESIGN.SPOTDESCRIPTOR.SPOTDECODESPEC) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR: Sets the value of the spotdecodespec property.
setSPOTDESCRIPTOR(ExperimentType.DESIGN.SPOTDESCRIPTOR) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN: Sets the value of the spotdescriptor property.
setSpotDesignReadSpec(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field spotDesignReadSpec.
setSql(Statement) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: Setter for the field sql.
setStart(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setStart(long) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setStart(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Setter for the field start.
setStartDate(Date) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field startDate.
setStartPage(String) - Method in class net.sourceforge.solexatools.util.PageInfo: Setter for the field startPage.
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition: Setter for the field startPosition.
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel: Setter for the field startPosition.
setStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field startPosition.
setState(CreateUpdateManager.State) - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
setState(String) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field state.
setStats(HashMap) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Setter for the field stats.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field status.
setStatus(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field status.
setStatusCmd(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field statusCmd.
setStatusCounts(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools: Setter for the field statusCounts.
setStatuses(String[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field statuses.
setStderr(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field stderr.
setStdErr(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field stdErr.
setStderr(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field stderr.
setStderr(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware: setStderr.
setStderrFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module: Added by Xiaoshu Wang: Setter for the file that will be used to redirect stderr
setStdout(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field stdout.
setStdOut(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field stdOut.
setStdout(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field stdout.
setStdout(File) - Method in interface net.sourceforge.seqware.pipeline.module.RedirectAware: setStdout.
setStdoutFile(File) - Method in class net.sourceforge.seqware.pipeline.module.Module: Setter for the field stdoutFile.
setStop(long) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setStop(long) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setStop(int) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Setter for the field stop.
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.ContigPosition: Setter for the field stopPosition.
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel: Setter for the field stopPosition.
setStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field stopPosition.
setStore(Store) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field store.
setStore(BerkeleyDBStore) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.CoverageProcessor: Setter for the field store.
setStore(Store) - Method in class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Setter for the field store.
setStoreType(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field storeType.
setStrand(QueryEngine.FeaturePB.StrandPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setStrand(Feature.Strand) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setStrand(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field strand.
setStrand(char) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field strand.
setStrategy(LibraryStrategy) - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: Setter for the field strategy.
setStrExpectedNumberReads(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field strExpectedNumberReads.
setStrExpectedNumberRuns(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field strExpectedNumberRuns.
setStrExpectedNumReads(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field strExpectedNumReads.
setStrExpectedNumRuns(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field strExpectedNumRuns.
setStrLaneCount(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunWizardDTO: Setter for the field strLaneCount.
setStrRefLane(String) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field strRefLane.
setStrStartURL(String) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field strStartURL.
setStrStartURL(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field strStartURL.
setStudies(Set<Study>) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field studies.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.FileReportRow: Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.SequencerRunReportId: Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyAttribute: Setter for the field study.
setStudy(Study) - Method in class net.sourceforge.seqware.common.model.StudyLink: Setter for the field study.
setStudy(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setStudy.
setSTUDYABSTRACT(JAXBElement<String>) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Sets the value of the studyabstract property.
setStudyAttributeId(int) - Method in class net.sourceforge.seqware.common.model.StudyAttribute: Setter for the field studyAttributeId.
setStudyAttributes(Set<StudyAttribute>) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field studyAttributes.
setSTUDYATTRIBUTES(StudyType.STUDYATTRIBUTES) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Sets the value of the studyattributes property.
setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: Setter for the field studyDAO.
setStudyDAO(StudyDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: setStudyDAO.
setStudyDAO(StudyDAO) - Method in interface net.sourceforge.seqware.common.business.StudyService: setStudyDAO.
setSTUDYDESCRIPTION(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Sets the value of the studydescription property.
setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy: Setter for the field studyId.
setStudyId(Integer) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field studyId.
setStudyLinkId(int) - Method in class net.sourceforge.seqware.common.model.StudyLink: Setter for the field studyLinkId.
setStudyLinks(Set<StudyLink>) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field studyLinks.
setSTUDYLINKS(StudyType.STUDYLINKS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType: Sets the value of the studylinks property.
setSTUDYREF(AnalysisType.PARENT.STUDYREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT: Sets the value of the studyref property.
setSTUDYREF(ExperimentType.STUDYREF) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the studyref property.
setStudyService(StudyService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.validation.StudyValidator: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.BulkDownloadListDetailsController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentSetupController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowListDetailsController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field studyService.
setStudyService(StudyService) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Setter for the field studyService.
setStudySwas(Set<String>) - Method in class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
setSTUDYTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Sets the value of the studytitle property.
setStudyType(StudyType) - Method in class net.sourceforge.seqware.common.model.Lane
setSTUDYTYPE(StudyType.DESCRIPTOR.STUDYTYPE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR: Sets the value of the studytype property.
setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: Setter for the field studyTypeDAO.
setStudyTypeDAO(StudyTypeDAO) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: setStudyTypeDAO.
setStudyTypeDAO(StudyTypeDAO) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: setStudyTypeDAO.
setStudyTypeId(Integer) - Method in class net.sourceforge.seqware.common.model.StudyType: Setter for the field studyTypeId.
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.seqware.common.ContextImpl
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: Setter for the field studyTypeService.
setStudyTypeService(StudyTypeService) - Method in class net.sourceforge.solexatools.webapp.controller.StudySetupController: Setter for the field studyTypeService.
setSubmissionComment(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the submissionComment property.
setSubmissionDate(XMLGregorianCalendar) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the submissionDate property.
setSubmissionId(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the submissionId property.
setSum(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Coverage: Setter for the field sum.
setSummaryLines(List<SummaryLine>) - Method in class net.sourceforge.solexatools.util.SummaryData: Setter for the field summaryLines.
setSUPPRESS(SubmissionType.ACTIONS.ACTION.SUPPRESS) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Sets the value of the suppress property.
setSvType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field svType.
setSwa(Integer) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field swa.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Invoice: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareFile: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareLane: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareSample: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareStudy: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field swAccession.
setSwAccession(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field swAccession.
setSwCluster(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Environment
setTag(String) - Method in interface net.sourceforge.seqware.common.model.Attribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Setter for the field tag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field tag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Setter for the field tag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: setTag.
setTag(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag: Setter for the field tag.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE: Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE: Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE: Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE: Sets the value of the tag property.
setTAG(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE: Sets the value of the tag property.
setTagACL(ACL, Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setTagACL.
setTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB.Builder
setTags(int, QESupporting.TagPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setTags(int, QESupporting.TagPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB.Builder
setTags(String) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field tags.
setTags(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field tags.
setTags(Map<String, String>) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set the key-value properties from metadata.xml
setTags(HashMap<String, String>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Model: setTags.
setTags(HashMap<String, String>) - Method in interface net.sourceforge.seqware.queryengine.backend.model.ModelInterface: setTags.
setTags(HashMap<String, String>) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: setTags.
setTagSet(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setTagSet(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setTagSet(TagSet) - Method in class com.github.seqware.queryengine.model.Tag.Builder
setTagSet(SGID) - Method in class com.github.seqware.queryengine.model.Tag.Builder
setTagSet(SGID) - Method in class com.github.seqware.queryengine.model.Tag: Set the TagSet for this particular tag, should not be called outside of the back-end.
setTagSet(TagSet) - Method in class com.github.seqware.queryengine.model.Tag: Set the TagSet for this particular tag, should not be called outside of the back-end.
setTagSetACL(ACL, TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setTagSetACL.
setTagSetIDs(List<SGID>) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field tagSetIDs.
setTagSpec(String) - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: Setter for the field tagSpec.
setTagSpecIDs(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setTagSpecIDs(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB.Builder
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD: Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY: Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE: Sets the value of the target property.
setTarget(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS: Sets the value of the target property.
setTaskGroup(boolean) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field taskGroup.
setTAXONID(Integer) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME: Sets the value of the taxonid property.
setTemplate(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field template.
setTemplate(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field template.
setTemplateFile(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: Setter for the field templateFile.
setTemplatePath(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field templatePath.
setTemplateType(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Setter for the field templateType.
setTest(Boolean) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setTestCmd(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field testCmd.
setThickEnd(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field thickEnd.
setThickStart(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field thickStart.
setThreads(int) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob
setThreads(int) - Method in interface net.sourceforge.seqware.pipeline.workflowV2.model.Job: set the max thread number
setTimestamp(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB.Builder
setTimestamp(Date) - Method in class com.github.seqware.queryengine.model.impl.AtomImpl: Set the clientTimestamp, this should never be called outside of the backend
setTimeTaken(String) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field timeTaken.
SETTINGSFILENOTFOUND - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant SETTINGSFILENOTFOUND=13
setTissSource(String) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Setter for the field tissSource.
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field title.
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field title.
setTitle(String) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field title.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType: Sets the value of the title property.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType: Sets the value of the title property.
setTITLE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType: Sets the value of the title property.
setTombstone(boolean) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB.Builder
setTombstone(boolean) - Method in class com.github.seqware.queryengine.util.FSGID: Back-end method for Features stored within high capacity featuresets
setTotal(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid: Setter for the field total.
setTotalDataBlocks(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType: Sets the value of the totalDataBlocks property.
setTotalPrice(Double) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field totalPrice.
setTotalReads(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the totalReads property.
setTotalSpots(BigInteger) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK: Sets the value of the totalSpots property.
setTotalUnits(Double) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field totalUnits.
setTRANSCRIPTASSEMBLY(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the transcriptassembly property.
setTranscriptId(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Feature: Setter for the field transcriptId.
setTRANSCRIPTSEQUENCING(Object) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE: Sets the value of the transcriptsequencing property.
setTranslatedSequence(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Consequence: Setter for the field translatedSequence.
setTranslocationDestinationContig(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field translocationDestinationContig.
setTranslocationDestinationStartPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field translocationDestinationStartPosition.
setTranslocationDestinationStopPosition(int) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field translocationDestinationStopPosition.
setTranslocationType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field translocationType.
setTreeAdaptor(TreeAdaptor) - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: setTreeAdaptor.
setTTL(long, boolean) - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet: Convenience method to set the expiry time
setTTL(int, boolean) - Method in class com.github.seqware.queryengine.model.impl.AbstractMolSet: Convenience method to set the expiry time for roughly hours ahead
setTTL(long, boolean) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Convenience method to set the expiry time
setTTL(int, boolean) - Method in class com.github.seqware.queryengine.model.impl.MoleculeImpl: Convenience method to set the expiry time for roughly hours ahead
setTTL(long, boolean) - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable: Convenience method to set the expiry time
setTTL(int, boolean) - Method in interface com.github.seqware.queryengine.model.interfaces.TTLable: Convenience method to set the expiry time for roughly hours ahead
setType(String) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.Builder
setType(String) - Method in class com.github.seqware.queryengine.model.Feature.Builder
setType(String) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setType(Requirement.Type) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
setType(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
setType(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field type.
setType(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Setter for the field type.
setType(String) - Method in class net.sourceforge.solexatools.webapp.controller.SearchController: Setter for the field type.
setTypeNode(String) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field typeNode.
setUnit(String) - Method in interface net.sourceforge.seqware.common.model.Attribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: setUnit.
setUnit(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Setter for the field unit.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute: Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute: Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: Setter for the field units.
setUnits(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute: Setter for the field units.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE: Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE: Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE: Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE: Sets the value of the units property.
setUNITS(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE: Sets the value of the units property.
setup(Mapper<ImmutableBytesWritable, Result, KEYOUT, VALUEOUT>.Context) - Method in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper
setup(String) - Static method in class net.sourceforge.seqware.common.util.freemarker.Freemarker: setup.
setup(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLBulkWriterStore: setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.PostgreSQLStore: setup.
setup(SeqWareSettings) - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: setup.
setup(SeqWareSettings) - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: setup.
setup(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: This allows you to search for different types of data in the metadb not just query engine databases
setup() - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: setup.
setup(ArrayList) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: setup.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Experiment: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Project: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Registration: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Sample: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareStudy: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Study: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field updateTimestamp.
setUpdateTimestamp(Date) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field updateTimestamp.
setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field updateTimeStamp.
setUpdateTimeStamp(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field updateTimeStamp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareExperiment: Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareFile: Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareLane: Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareProcessing: Setter for the field updateTstmp.
setUpdateTstmp(Date) - Method in class net.sourceforge.seqware.common.model.ShareSample: Setter for the field updateTstmp.
setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field updateValidator.
setUpdateValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: setUpdateValidator.
setupDirectory() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: to be Overridden by the workflow author
setupEnvironment() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: to be Overridden by the workflow author generally people don't override this.
setupFiles() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: to be Overridden by the workflow author the place to specify inputs and outputs to the program also, a user can specify inputs and outputs on jobs directly in which case they are still provisioned properly with respect to the job (inputs before, outputs after) when you define inputs/outputs here they are provisioned before all jobs and after all jobs respectively
setupWorkflow() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: to be Overridden by the workflow author you generally don't call this as the workflow author since it promotes hardcoding this will typically be filled in by maven
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ExperimentLink: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.IUSLink: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.LaneLink: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingExperiments: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingIus: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingLanes: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSamples: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingSequencerRuns: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.ProcessingStudies: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.SampleLink: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.model.StudyLink: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setUrl(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Pfn: Setter for the field url.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK: Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK: Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK: Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK: Sets the value of the url property.
setURL(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK: Sets the value of the url property.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.FileDto: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.IusDto: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.LibraryDto: Setter for the field url.
setUrl(String) - Method in class net.sourceforge.seqware.webservice.dto.SampleSearchDto: Setter for the field url.
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.File: Setter for the field urlLabel.
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field urlLabel.
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.FileMetadata
setUrlLabel(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field urlLabel.
setURLLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK: Sets the value of the urllink property.
setURLLINK(ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK: Sets the value of the urllink property.
setURLLINK(RunType.RUNLINKS.RUNLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK: Sets the value of the urllink property.
setURLLINK(SampleType.SAMPLELINKS.SAMPLELINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK: Sets the value of the urllink property.
setURLLINK(StudyType.STUDYLINKS.STUDYLINK.URLLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK: Sets the value of the urllink property.
setUrlString(String) - Method in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource: Setter for the field urlString.
setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRun: Setter for the field useIparIntensities.
setUseIparIntensities(Boolean) - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO: Setter for the field useIparIntensities.
setUseOneURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field useOneURL.
setUser(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
setUser(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB.Builder
setUsername(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field username.
setUserName(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field userName.
setUsername(String) - Method in class net.sourceforge.seqware.queryengine.backend.util.SeqWareSettings: Setter for the field username.
setUsers(int, QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setUsers(int, QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB.Builder
setUseTwoURL(Boolean) - Method in class net.sourceforge.seqware.common.model.UploadSequence: Setter for the field useTwoURL.
setUseURL(Boolean) - Method in class net.sourceforge.seqware.common.business.UploadFile: Setter for the field useURL.
setUuid(UUID) - Method in class com.github.seqware.queryengine.util.SGID: Setter for the field uuid.
setVALIDATE(SubmissionType.ACTIONS.ACTION.VALIDATE) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION: Sets the value of the validate property.
setValidationReportService(ValidationReportService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field validationReportService.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ExperimentController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.FileController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.LaneController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.ProcessingController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.RegistrationController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SampleController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.SequencerRunControllerDTO: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.StudyController: setValidator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadFileController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Setter for the field validator.
setValidator(Validator) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Setter for the field validator.
setValue(Object) - Method in class com.github.seqware.queryengine.model.Tag.Builder: Set the value to one of ValueType
setValue(String) - Method in interface net.sourceforge.seqware.common.model.Attribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.ExperimentAttribute: Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.FileAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.IUSAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.LaneAttribute: Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.ProcessingAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.SampleSearchAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.StudyAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: setValue.
setValue(String) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Argument: Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.JobProfile: Setter for the field value.
setValue(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Requirement
setValue(String) - Method in class net.sourceforge.seqware.queryengine.backend.model.Tag: Setter for the field value.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE: Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE: Sets the value of the value property.
setValue(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR: Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE: Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE: Sets the value of the value property.
setVALUE(String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE: Sets the value of the value property.
setValue(String) - Method in class net.sourceforge.seqware.webservice.dto.AttributeDto: Setter for the field value.
setValues(SortedSet<WorkflowParamValue>) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field values.
setVBytes(ByteString) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setVDouble(double) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setVerbose(boolean) - Method in class net.sourceforge.seqware.common.util.filetools.ProvisionFilesUtil: Enable class verbose mode.
setVerbose(boolean) - Static method in class net.sourceforge.seqware.common.util.Log: override the log4j.properties
setVersion(String) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.common.module.ReturnValue: Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field version.
setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set workflow version
setVersion(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
setVFloat(float) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setVInteger(int) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setVisibleParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.solexatools.util.SummaryData: Setter for the field visibleParams.
setVLong(long) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setVSGIDRef(QESupporting.SGIDPB) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setVSGIDRef(QESupporting.SGIDPB.Builder) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setVString(String) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB.Builder
setWait(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: wait for the workflow to finished, user can override this by using --wait from command line
setWfRuns(WorkflowRun[]) - Method in class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Setter for the field wfRuns.
setWidth(int) - Method in class net.sourceforge.solexatools.webapp.metamodel.Flexigrid.ColumnModel
setWithHasFile(SortedSet<Experiment>) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: setWithHasFile.
setWithHasFile(Set<File>, String) - Method in interface net.sourceforge.seqware.common.business.FileService: setWithHasFile.
setWithHasFile(SortedSet<Experiment>) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: setWithHasFile.
setWithHasFile(Set<File>, String) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: setWithHasFile.
setWithHasFile(SortedSet<IUS>) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: setWithHasFile.
setWithHasFile(SortedSet<Lane>) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: setWithHasFile.
setWithHasFile(Set<Processing>) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: setWithHasFile.
setWithHasFile(Set<Processing>, String) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: setWithHasFile.
setWithHasFile(Integer, SortedSet<Sample>) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: setWithHasFile.
setWithHasFile(SortedSet<IUS>) - Method in interface net.sourceforge.seqware.common.business.IUSService: setWithHasFile.
setWithHasFile(SortedSet<Lane>) - Method in interface net.sourceforge.seqware.common.business.LaneService: setWithHasFile.
setWithHasFile(Set<Processing>) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: setWithHasFile.
setWithHasFile(Set<Processing>, String) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: setWithHasFile.
setWithHasFile(Integer, SortedSet<Sample>) - Method in interface net.sourceforge.seqware.common.business.SampleService: setWithHasFile.
setWorkerName(String) - Method in class com.github.seqware.queryengine.system.importers.workers.ImportWorker: Setter for the field workerName.
setWorkerName(String) - Method in class net.sourceforge.seqware.queryengine.tools.importers.workers.ImportWorker: Setter for the field workerName.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.SampleReportRow: Setter for the field workflow.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowAttribute: Setter for the field workflow.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field workflow.
setWorkflow(Workflow) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field workflow.
setWorkflow_accession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set workflow_accession
setWorkflow_run_accession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: set workflow run accession
setWorkflowAccession(int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field workflowAccession.
setWorkflowAccession(String) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setWorkflowAccessionsToCheck(Set<String>) - Method in class net.sourceforge.seqware.pipeline.deciders.BasicDecider
setWorkflowAttributes(Set<WorkflowAttribute>) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field workflowAttributes.
setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel
setWorkflowBundleDir(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow: set the workflowBundle directory
setWorkflowDAO(WorkflowDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: setWorkflowDAO.
setWorkflowDAO(WorkflowDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: setWorkflowDAO.
setWorkflowDir(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: Setter for the field workflowDir.
setWorkflowId(Integer) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field workflowId.
setWorkflowParam(WorkflowParam) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Setter for the field workflowParam.
setWorkflowParamDAO(WorkflowParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: setWorkflowParamDAO.
setWorkflowParamDAO(WorkflowParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: setWorkflowParamDAO.
setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParam: Setter for the field workflowParamId.
setWorkflowParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Setter for the field workflowParamId.
setWorkflowParams(SortedSet<WorkflowParam>) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field workflowParams.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field workflowParamService.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Setter for the field workflowParamService.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController: Setter for the field workflowParamService.
setWorkflowParamService(WorkflowParamService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController: Setter for the field workflowParamService.
setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: setWorkflowParamValueDAO.
setWorkflowParamValueDAO(WorkflowParamValueDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: setWorkflowParamValueDAO.
setWorkflowParamValueId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue: Setter for the field workflowParamValueId.
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field workflowParamValueService.
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Setter for the field workflowParamValueService.
setWorkflowParamValueService(WorkflowParamValueService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController: Setter for the field workflowParamValueService.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Expense: Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunAttribute: Setter for the field workflowRun.
setWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: Setter for the field workflowRun.
setWorkflowRun(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setWorkflowRun.
setWorkflowRunAccession(String) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
setWorkflowRunAncesstor(boolean) - Method in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
setWorkflowRunAttributes(Set<WorkflowRunAttribute>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field workflowRunAttributes.
setWorkflowRunByAncestorWorkflowRunId(WorkflowRun) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field workflowRunByAncestorWorkflowRunId.
setWorkflowRunDAO(WorkflowRunDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: setWorkflowRunDAO.
setWorkflowRunDAO(WorkflowRunDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: setWorkflowRunDAO.
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.Processing: Setter for the field workflowRunId.
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun: Setter for the field workflowRunId.
setWorkflowRunId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field workflowRunId.
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: setWorkflowRunParamDAO.
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: Setter for the field workflowRunParamDAO.
setWorkflowRunParamDAO(WorkflowRunParamDAO) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: setWorkflowRunParamDAO.
setWorkflowRunParamId(Integer) - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: setWorkflowRunParamId.
setWorkflowRunParams(SortedSet<WorkflowRunParam>) - Method in class net.sourceforge.seqware.common.model.WorkflowRun: Setter for the field workflowRunParams.
setWorkflowRunProcessings(Collection<Processing>) - Method in class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow: Setter for the field workflowRunProcessings.
setWorkflowRunRunning(Integer, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setWorkflowRunRunning.
setWorkflowRunRunningWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setWorkflowRunRunningWithSample.
setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.IUS: Setter for the field workflowRuns.
setWorkflowRuns(Set<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Lane: Setter for the field workflowRuns.
setWorkflowRuns(SortedSet<WorkflowRun>) - Method in class net.sourceforge.seqware.common.model.Workflow: Setter for the field workflowRuns.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysBulkDownloadListDetailsController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysEventController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListDetailsController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysRunningListDetailsController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.CancelAnalysisWorkflowController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.DownloadFileListController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SampleWorkflowRunsController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputListController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Setter for the field workflowRunService.
setWorkflowRunService(WorkflowRunService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController: Setter for the field workflowRunService.
setWorkflowRunWithSample(HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.SetNodeIdInSession: setWorkflowRunWithSample.
setWorkflows(ArrayList<WorkflowInfo>) - Method in class net.sourceforge.seqware.pipeline.bundle.BundleInfo: Setter for the field workflows.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.seqware.common.ContextImpl: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysListController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.AnalisysTableControllerDetails: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ChangeWorkflowParamValueController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.EntityController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.LaunchWorkflowSetupController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SearchResultsListController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SelectInputController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController: Setter for the field workflowService.
setWorkflowService(WorkflowService) - Method in class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController: Setter for the field workflowService.
setWorkflowSqwVersion(String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo: setWorkflowSqwVersion.
setXREFLINK(AnalysisType.ANALYSISLINKS.ANALYSISLINK.XREFLINK) - Method in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK: Sets the value of the xreflink property.
setZygosity(byte) - Method in class net.sourceforge.seqware.queryengine.backend.model.Variant: Setter for the field zygosity.
SGID - Class in com.github.seqware.queryengine.util: A wrapper for our eventual choice of globally unique primary key which may or may not be UUIDs.
SGID() - Constructor for class com.github.seqware.queryengine.util.SGID: Create a new SGID
SGID(String) - Constructor for class com.github.seqware.queryengine.util.SGID: Generate a SGID that can look up things given only a rowKey.
SGID(SGID) - Constructor for class com.github.seqware.queryengine.util.SGID: Clone a given SGID
SGID(long, long, long, String) - Constructor for class com.github.seqware.queryengine.util.SGID: Back-end constructor, create a fully functional SGID
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
SGID_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
SGIDIO - Class in com.github.seqware.queryengine.impl.protobufIO: SGIDIO class.
SGIDIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.SGIDIO
SGIDIterable<T extends Atom> - Class in com.github.seqware.queryengine.util: A bit of a hack class, allows us to have getCount as well as iterable
SGIDIterable(Iterable<SGID>, Class<T>) - Constructor for class com.github.seqware.queryengine.util.SGIDIterable: Constructor for SGIDIterable.
SGIDIterable.SGIDIterator - Class in com.github.seqware.queryengine.util
SGIDIterable.SGIDIterator() - Constructor for class com.github.seqware.queryengine.util.SGIDIterable.SGIDIterator
SGIDTB - Class in com.github.seqware.queryengine.impl.tuplebinderIO: SGIDTB class.
SGIDTB() - Constructor for class com.github.seqware.queryengine.impl.tuplebinderIO.SGIDTB
ShareExperiment - Class in net.sourceforge.seqware.common.model: ShareExperiment generated by hbm2java
ShareExperiment() - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment: Constructor for ShareExperiment.
ShareExperiment(int, Experiment, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment: Constructor for ShareExperiment.
ShareExperiment(int, Experiment, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareExperiment: Constructor for ShareExperiment.
ShareExperimentDAO - Interface in net.sourceforge.seqware.common.dao: ShareExperimentDAO interface.
ShareExperimentDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ShareExperimentDAOHibernate class.
ShareExperimentDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate
ShareExperimentService - Interface in net.sourceforge.seqware.common.business: ShareExperimentService interface.
ShareExperimentServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ShareExperimentServiceImpl class.
ShareExperimentServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl
ShareFile - Class in net.sourceforge.seqware.common.model: ShareFile generated by hbm2java
ShareFile() - Constructor for class net.sourceforge.seqware.common.model.ShareFile: Constructor for ShareFile.
ShareFile(int, File, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile: Constructor for ShareFile.
ShareFile(int, File, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareFile: Constructor for ShareFile.
ShareFileDAO - Interface in net.sourceforge.seqware.common.dao: ShareFileDAO interface.
ShareFileDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ShareFileDAOHibernate class.
ShareFileDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate
ShareFileService - Interface in net.sourceforge.seqware.common.business: ShareFileService interface.
ShareFileServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ShareFileServiceImpl class.
ShareFileServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl
ShareLane - Class in net.sourceforge.seqware.common.model: ShareLane generated by hbm2java
ShareLane() - Constructor for class net.sourceforge.seqware.common.model.ShareLane: Constructor for ShareLane.
ShareLane(int, Lane, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane: Constructor for ShareLane.
ShareLane(int, Lane, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareLane: Constructor for ShareLane.
ShareLaneDAO - Interface in net.sourceforge.seqware.common.dao: ShareLaneDAO interface.
ShareLaneDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ShareLaneDAOHibernate class.
ShareLaneDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate
ShareLaneService - Interface in net.sourceforge.seqware.common.business: ShareLaneService interface.
ShareLaneServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ShareLaneServiceImpl class.
ShareLaneServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl
ShareProcessing - Class in net.sourceforge.seqware.common.model: ShareProcessing generated by hbm2java
ShareProcessing() - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing: Constructor for ShareProcessing.
ShareProcessing(int, Processing, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing: Constructor for ShareProcessing.
ShareProcessing(int, Processing, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareProcessing: Constructor for ShareProcessing.
ShareProcessingDAO - Interface in net.sourceforge.seqware.common.dao: ShareProcessingDAO interface.
ShareProcessingDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ShareProcessingDAOHibernate class.
ShareProcessingDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate
ShareProcessingService - Interface in net.sourceforge.seqware.common.business: ShareProcessingService interface.
ShareProcessingServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ShareProcessingServiceImpl class.
ShareProcessingServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl
ShareSample - Class in net.sourceforge.seqware.common.model: ShareSample generated by hbm2java
ShareSample() - Constructor for class net.sourceforge.seqware.common.model.ShareSample: Constructor for ShareSample.
ShareSample(int, Sample, Registration, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample: Constructor for ShareSample.
ShareSample(int, Sample, Registration, Boolean, Integer, Date, Date) - Constructor for class net.sourceforge.seqware.common.model.ShareSample: Constructor for ShareSample.
ShareSampleDAO - Interface in net.sourceforge.seqware.common.dao: ShareSampleDAO interface.
ShareSampleDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ShareSampleDAOHibernate class.
ShareSampleDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate
ShareSampleService - Interface in net.sourceforge.seqware.common.business: ShareSampleService interface.
ShareSampleServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ShareSampleServiceImpl class.
ShareSampleServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl
ShareStudy - Class in net.sourceforge.seqware.common.model: ShareStudy class.
ShareStudy() - Constructor for class net.sourceforge.seqware.common.model.ShareStudy: Constructor for ShareStudy.
ShareStudyDAO - Interface in net.sourceforge.seqware.common.dao: ShareStudyDAO interface.
ShareStudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ShareStudyDAOHibernate class.
ShareStudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: Constructor for ShareStudyDAOHibernate.
ShareStudyService - Interface in net.sourceforge.seqware.common.business: ShareStudyService interface.
ShareStudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ShareStudyServiceImpl class.
ShareStudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: Constructor for ShareStudyServiceImpl.
ShareValidatorController - Class in net.sourceforge.solexatools.webapp.controller: ShareValidatorController class.
ShareValidatorController() - Constructor for class net.sourceforge.solexatools.webapp.controller.ShareValidatorController: Constructor for ShareValidatorController.
ShareWorkflowRun - Class in net.sourceforge.seqware.common.model: ShareWorkflowRun class.
ShareWorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.ShareWorkflowRun: Constructor for ShareWorkflowRun.
ShareWorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao: ShareWorkflowRunDAO interface.
ShareWorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: ShareWorkflowRunDAOHibernate class.
ShareWorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: Constructor for ShareWorkflowRunDAOHibernate.
ShareWorkflowRunService - Interface in net.sourceforge.seqware.common.business: ShareWorkflowRunService interface.
ShareWorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl: ShareWorkflowRunServiceImpl class.
ShareWorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: Constructor for ShareWorkflowRunServiceImpl.
SignUpController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
SignUpController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SignUpController: Constructor for SignUpController.
SimpleFileLock - Class in net.sourceforge.seqware.common.util.filetools.lock: Deprecated.
SimpleFileLock(String) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock: Deprecated. Constructor for SimpleFileLock.
SimpleFileLock(File) - Constructor for class net.sourceforge.seqware.common.util.filetools.lock.SimpleFileLock: Deprecated. Constructor for SimpleFileLock.
SimpleModelManager - Class in com.github.seqware.queryengine.impl: A Simple implementation of the CreateUpdateManager interface.
SimpleModelManager() - Constructor for class com.github.seqware.queryengine.impl.SimpleModelManager
SimpleModelManager.AtomStatePair - Class in com.github.seqware.queryengine.impl
SimpleModelManager.AtomStatePair(Atom, CreateUpdateManager.State) - Constructor for class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
SimplePersistentBackEnd - Class in com.github.seqware.queryengine.impl: A toy backend implementation that writes all stores objects to disk using Java persistence.
SimplePersistentBackEnd(StorageInterface) - Constructor for class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Constructor for SimplePersistentBackEnd.
single - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.LIBRARYDESCRIPTOR.LIBRARYLAYOUT
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3CreateFileURLs
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3DeleteFiles
size - Variable in class net.sourceforge.seqware.pipeline.modules.utilities.S3ListFiles
SIZE_COUNT_FILE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil: Constant SIZE_COUNT_FILE=5
SIZE_COUNT_TREE - Static variable in class net.sourceforge.solexatools.util.PaginationUtil: Constant SIZE_COUNT_TREE=20
sleep(int) - Static method in class net.sourceforge.seqware.common.util.processtools.ProcessTools: sleep.
SNV - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SNV=1
SNVMix - Class in net.sourceforge.seqware.pipeline.modules: Syntax: ./SNVMix2 -m [-i ] [-o ] [-T | -C | -F] [-p < q | m | s >] [-t < mb | m | b | M | Mb | MB | SNVMix1>] [-q <#>] [-Q <#>] [-a/-b/-d <#,#,#>] [-M ] [-h] Required: -m model file, a line for mu and a line for pi, three space-separated values each, like: mu 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx pi 0.xxxxxxxx 0.xxxxxxxx 0.xxxxxxxx Optional: -i quality pileup, from pileup2matlab.pl script (def: STDIN) -o where to put the results (def: STDOUT) -T | -C | -F Train, Classify or Filter (def: Classify) -p q|m|s Input pileup format (def: s) q = quality m = MAQ s = SAMtools -t mb|m|b|M|Mb|MB|SNVMix1 Filter type (def: mb) mb Lowest between map and base quality m Filter on map, and use as surrogate for base quality b Filter on base quality, take map quality as 1 M Filter on map quality but use only base quality Mb Filter on map quality and use both map and base qualities MB Filter on map quality AND base quality SNVMix1 Filter on base quality and map quality, afterwards consider them perfect -q # Cutoff Phred value for Base Quality, anything <= this value is ignored (def: Q19) -Q # Cutoff Phred value for Map Quality, anything <= this value is ignored (def: Q19) Training parameters: -a #,#,# Provide alpha training parameters -b #,#,# Provide beta training parameters -d #,#,# Provide delta training parameters -M Provide a file containing training parameters (will override -a, -b and -d) Values are space-separated: alpha # # # beta # # # delta # # # -apply-filter -perl-path Path to perl installation -filter-path Path to the filter script -threshold THRESHOLD is given, then SNVs will be reported when the selected probability exceeds this -c [2|3] TYPE is the number of classes to consider '2' considers only AA and {AB U BB} (default) '3' considers AA, AB and BB -h this message
SNVMix() - Constructor for class net.sourceforge.seqware.pipeline.modules.SNVMix
SOFeatureImporter - Class in com.github.seqware.queryengine.system.importers: Importer using a new interface to the parameters in order to support SO importing and the specification of a tag set and reference to attach to.
SOFeatureImporter() - Constructor for class com.github.seqware.queryengine.system.importers.SOFeatureImporter
someString() - Method in class net.sourceforge.seqware.webservice.resources.tables.LibraryResource: someString.
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant SORT_NAME="sortname"
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Constant SORT_NAME="sortname"
SORT_NAME - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant SORT_NAME="sortname"
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant SORT_ORDER="sortorder"
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Constant SORT_ORDER="sortorder"
SORT_ORDER - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant SORT_ORDER="sortorder"
SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant SORT_ORDER_ASC="asc"
SORT_ORDER_ASC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant SORT_ORDER_ASC="asc"
SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant SORT_ORDER_DESC="desc"
SORT_ORDER_DESC - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant SORT_ORDER_DESC="desc"
source - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
source - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
SOURCE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
sourceSet - Variable in class com.github.seqware.queryengine.plugins.hbasemr.QEMapper: the feature set that we will be reading
SpliceJunctionCounts - Class in net.sourceforge.seqware.pipeline.modules.quantification: Calculate counts per junction given a BAM file of aligned reads and a list of splice junctions.
SpliceJunctionCounts() - Constructor for class net.sourceforge.seqware.pipeline.modules.quantification.SpliceJunctionCounts
splitFile(File, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: splitFile.
spotdecodemethod - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
spotdecodespec - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN.SPOTDESCRIPTOR
spotdescriptor - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.DESIGN
SQLQUERYFAILED - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant SQLQUERYFAILED=82
SqwFile - Class in net.sourceforge.seqware.pipeline.workflowV2.model: a file object which has all information for provision
SqwFile() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.SqwFile
SRF2Fastq - Class in net.sourceforge.seqware.pipeline.modules.io: SRF2Fastq class.
SRF2Fastq() - Constructor for class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq
srf2fastq - Class in net.sourceforge.seqware.pipeline.modules: srf2fastq class.
srf2fastq() - Constructor for class net.sourceforge.seqware.pipeline.modules.srf2fastq
SRF2Fastq_0_7_2 - Class in net.sourceforge.seqware.pipeline.modules.io: SRF2Fastq_0_7_2 class.
SRF2Fastq_0_7_2() - Constructor for class net.sourceforge.seqware.pipeline.modules.io.SRF2Fastq_0_7_2
stackTraceToString(Throwable) - Static method in class net.sourceforge.seqware.common.util.exceptiontools.ExceptionTools: stackTraceToString.
START_ALL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant START_ALL_QUERYDATELONG="start-ALL_query-date-long"
START_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
START_PMC_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant START_PMC_QUERYDATELONG="start-PMC_query-date-long"
START_PMCSI_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant START_PMCSI_QUERYDATELONG="start-PMCSI_query-date-long"
START_QUAL_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant START_QUAL_QUERYDATELONG="start-QUAL_query-date-long"
startCommand(Map<String, String>, String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: startCommand.
startCommand(String) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: startCommand.
startCommand(String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: startCommand.
startCommand(Map<String, String>, String[]) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: An alternate runner that launches a process and returns it so that the caller can process it's output directly.
STARTCOUNTDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant STARTCOUNTDATELONG="start-count-date-long"
STARTDUMP_QUERYDATELONG - Static variable in class com.github.seqware.queryengine.tutorial.PosterStatCompiler: Constant STARTDUMP_QUERYDATELONG="start-dump_query-date-long"
startPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
startPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
startTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: startTransaction.
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.BerkeleyDBStore: startTransaction.
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore: startTransaction.
startTransaction() - Method in class net.sourceforge.seqware.queryengine.backend.store.Store: startTransaction.
startTransaction() - Method in interface net.sourceforge.seqware.queryengine.backend.store.StoreInterface: startTransaction.
status - Variable in exception net.sourceforge.seqware.common.util.ExitException
statusCounts - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
stderr - Variable in class net.sourceforge.seqware.common.module.ReturnValue
stderr(String) - Static method in class net.sourceforge.seqware.common.util.Log: stderr.
StdErr - Class in net.sourceforge.seqware.common.util.processtools.stderr: StdErr class.
StdErr() - Constructor for class net.sourceforge.seqware.common.util.processtools.stderr.StdErr
stderr2string(Process) - Static method in class net.sourceforge.seqware.common.util.processtools.stderr.StdErr: stderr2string.
StderrRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module: Annotation type to tag where to start Stderr redirect Created by IntelliJ IDEA.
stdout - Variable in class net.sourceforge.seqware.common.module.ReturnValue
stdout(String) - Static method in class net.sourceforge.seqware.common.util.Log: stdout.
StdOut - Class in net.sourceforge.seqware.common.util.processtools.stdout: StdOut class.
StdOut() - Constructor for class net.sourceforge.seqware.common.util.processtools.stdout.StdOut
stdout2file(Process, File, boolean) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut: stdout2file.
stdout2file(Process, ArrayList<File>, boolean, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut: stdout2file.
stdout2fileBinary(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut: stdout2fileBinary.
stdout2fileBinary(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut: stdout2fileBinary.
stdout2fileEncoded(Process, File) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut: stdout2fileEncoded.
stdout2fileEncoded(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut: stdout2fileEncoded.
stdout2fileEncodedStripQualPrimer(Process, ArrayList<File>, int) - Static method in class net.sourceforge.seqware.common.util.processtools.stdout.StdOut: stdout2fileEncodedStripQualPrimer.
STDOUTERR - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant STDOUTERR=90
StdoutRedirect - Annotation Type in net.sourceforge.seqware.pipeline.module: Interface for declaring when to do the Created by IntelliJ IDEA.
stop() - Static method in class net.sourceforge.seqware.queryengine.webservice.controller.SeqWareWebServiceMain: stop.
STOP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
stopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.LocatableModel
stopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
storage - Variable in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd
StorageInterface - Class in com.github.seqware.queryengine.impl: Defines a very basic interface that allows us to abstract whether we write to files or to databases or just keep things in memory
StorageInterface() - Constructor for class com.github.seqware.queryengine.impl.StorageInterface
store(Atom...) - Method in interface com.github.seqware.queryengine.impl.BackEndInterface: Store obj in the back-end.
store(Atom...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Store obj in the back-end.
Store - Class in net.sourceforge.seqware.queryengine.backend.store: Abstract Store class.
Store() - Constructor for class net.sourceforge.seqware.queryengine.backend.store.Store
StoreInterface - Interface in net.sourceforge.seqware.queryengine.backend.store: StoreInterface interface.
strand - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
strand - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
STRAND_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
STRING - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant STRING=24
STRING - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant STRING=24
STRINGID - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model: Constant STRINGID=20
StringId - Class in net.sourceforge.seqware.queryengine.backend.model: StringId class.
StringId() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.StringId
StringIdTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders: StringIdTB class.
StringIdTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.StringIdTB
StringUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus: StringUtils class.
StringUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.StringUtils
Study - Class in net.sourceforge.seqware.common.model
Study() - Constructor for class net.sourceforge.seqware.common.model.Study: Constructor for Study.
study - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudySet
STUDY_ATTRIBUTES - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant STUDY_ATTRIBUTES="Header.STUDY_ATTRIBUTES.getTitle()"
STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController: Constant STUDY_ID="study_id"
STUDY_ID - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant STUDY_ID="study_id"
STUDY_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant STUDY_PREFIX="study_"
STUDY_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant STUDY_SWA="Header.STUDY_SWA.getTitle()"
STUDY_TAG_PREFIX - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant STUDY_TAG_PREFIX="Header.STUDY_TAG_PREFIX.getTitle()"
STUDY_TITLE - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant STUDY_TITLE="Header.STUDY_TITLE.getTitle()"
STUDY_VIEW - Static variable in class net.sourceforge.solexatools.util.Constant: Constant STUDY_VIEW="redirect:/myStudyList.htm"
studyabstract - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
StudyAttribute - Class in net.sourceforge.seqware.common.model: StudyAttribute generated by hbm2java
StudyAttribute() - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute: Constructor for StudyAttribute.
StudyAttribute(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute: Constructor for StudyAttribute.
StudyAttribute(int, Study, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyAttribute: Constructor for StudyAttribute.
studyattribute - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
StudyAttributeDAO - Interface in net.sourceforge.seqware.common.dao: StudyAttributeDAO interface.
StudyAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: StudyAttributeDAOHibernate class.
StudyAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate
studyattributes - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
StudyBuildTree - Class in net.sourceforge.solexatools.util: StudyBuildTree class.
StudyBuildTree() - Constructor for class net.sourceforge.solexatools.util.StudyBuildTree
StudyController - Class in net.sourceforge.solexatools.webapp.controller: StudyController
StudyController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController: Constructor for StudyController.
StudyController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyController: Constructor for StudyController.
StudyDAO - Interface in net.sourceforge.seqware.common.dao: StudyDAO interface.
StudyDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: StudyDAOHibernate class.
StudyDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: Constructor for StudyDAOHibernate.
studydescription - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
StudyHtmlUtil - Class in net.sourceforge.solexatools.util: StudyHtmlUtil class.
StudyHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.StudyHtmlUtil
StudyIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries: StudyIdFilesResource class.
StudyIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesResource: Constructor for StudyIdFilesResource.
StudyIdFilesTSVResource - Class in net.sourceforge.seqware.webservice.resources.queries: StudyIdFilesTSVResource class.
StudyIdFilesTSVResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.StudyIdFilesTSVResource: Constructor for StudyIdFilesTSVResource.
StudyIDFilter - Class in net.sourceforge.seqware.webservice.resources.filters: StudyIDFilter class.
StudyIDFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.StudyIDFilter
StudyIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: StudyIDResource class.
StudyIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyIDResource: Constructor for StudyIDResource.
StudyLink - Class in net.sourceforge.seqware.common.model: StudyLink generated by hbm2java
StudyLink() - Constructor for class net.sourceforge.seqware.common.model.StudyLink: Constructor for StudyLink.
StudyLink(int, Study, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink: Constructor for StudyLink.
StudyLink(int, Study, String, String, String, String) - Constructor for class net.sourceforge.seqware.common.model.StudyLink: Constructor for StudyLink.
studylink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
StudyLinkDAO - Interface in net.sourceforge.seqware.common.dao: StudyLinkDAO interface.
StudyLinkDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: StudyLinkDAOHibernate class.
StudyLinkDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate
studylinks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType
StudyList - Class in net.sourceforge.seqware.common.model.lists: StudyList class.
StudyList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyList: Constructor for StudyList.
StudyListController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
StudyListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListController: Constructor for StudyListController.
StudyListDetailsController - Class in net.sourceforge.solexatools.webapp.controller: StudyListDetailsController class.
StudyListDetailsController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsController: Constructor for StudyListDetailsController.
StudyListDetailsFlatController - Class in net.sourceforge.solexatools.webapp.controller
StudyListDetailsFlatController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyListDetailsFlatController
studyref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.PARENT
studyref - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
StudyReportBoxController - Class in net.sourceforge.solexatools.webapp.controller: StudyReportBoxController class.
StudyReportBoxController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportBoxController
StudyReportController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
StudyReportController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportController: Constructor for StudyReportController.
StudyReportSetupController - Class in net.sourceforge.solexatools.webapp.controller: StudyReportSetupController class.
StudyReportSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportSetupController
StudyReportTableController - Class in net.sourceforge.solexatools.webapp.controller: StudyReportTableController class.
StudyReportTableController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constructor for StudyReportTableController.
StudyResource - Class in net.sourceforge.seqware.webservice.resources.tables: StudyResource class.
StudyResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyResource: Constructor for StudyResource.
StudySampleReportFileLineItem - Class in net.sourceforge.solexatools.webapp.metamodel: StudySampleReportFileLineItem class.
StudySampleReportFileLineItem(Sample, Sample, IUS, File) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportFileLineItem: Constructor for StudySampleReportFileLineItem.
StudySampleReportLineItem - Class in net.sourceforge.solexatools.webapp.metamodel: StudySampleReportLineItem class.
StudySampleReportLineItem(Sample, Sample, String[]) - Constructor for class net.sourceforge.solexatools.webapp.metamodel.StudySampleReportLineItem: Constructor for StudySampleReportLineItem.
StudyService - Interface in net.sourceforge.seqware.common.business: StudyService interface.
StudyServiceImpl - Class in net.sourceforge.seqware.common.business.impl: StudyServiceImpl class.
StudyServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: Constructor for StudyServiceImpl.
StudySet - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudySet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudySet
StudySetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController
StudySetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.StudySetupController: Constructor for StudySetupController.
studytitle - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
StudyType - Class in net.sourceforge.seqware.common.model: StudyType class.
StudyType() - Constructor for class net.sourceforge.seqware.common.model.StudyType
StudyType - Class in net.sourceforge.seqware.queryengine.webservice.model: A Study is a container for a sequencing investigation that may comprise multiple experiments.
StudyType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType
studytype - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
StudyType.DESCRIPTOR - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.DESCRIPTOR() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR
StudyType.DESCRIPTOR.STUDYTYPE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.DESCRIPTOR.STUDYTYPE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.DESCRIPTOR.STUDYTYPE
StudyType.STUDYATTRIBUTES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.STUDYATTRIBUTES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
StudyType.STUDYLINKS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.STUDYLINKS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS
StudyType.STUDYLINKS.STUDYLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.ENTREZLINK
StudyType.STUDYLINKS.STUDYLINK.URLLINK - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
StudyType.STUDYLINKS.STUDYLINK.URLLINK() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
StudyTypeDAO - Interface in net.sourceforge.seqware.common.dao: StudyTypeDAO interface.
StudyTypeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: StudyTypeDAOHibernate class.
StudyTypeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: Constructor for StudyTypeDAOHibernate.
StudyTypeList - Class in net.sourceforge.seqware.common.model.lists: StudyTypeList class.
StudyTypeList() - Constructor for class net.sourceforge.seqware.common.model.lists.StudyTypeList: Constructor for StudyTypeList.
StudyTypeResource - Class in net.sourceforge.seqware.webservice.resources.tables: ExperimentResource class.
StudyTypeResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.StudyTypeResource: Constructor for ExperimentResource.
StudyTypeService - Interface in net.sourceforge.seqware.common.business: StudyTypeService interface.
StudyTypeServiceImpl - Class in net.sourceforge.seqware.common.business.impl: StudyTypeServiceImpl class.
StudyTypeServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: Constructor for StudyTypeServiceImpl.
StudyUpdateValidator - Class in net.sourceforge.solexatools.validation
StudyUpdateValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyUpdateValidator
StudyValidator - Class in net.sourceforge.solexatools.validation: StudyValidator class.
StudyValidator() - Constructor for class net.sourceforge.solexatools.validation.StudyValidator: Constructor for StudyValidator.
subList(int, int, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil: subList.
subList(HttpServletRequest, String, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil: subList.
subList(HttpServletRequest, String, int, List<T>) - Static method in class net.sourceforge.solexatools.util.PaginationUtil: subList.
subListSD(HttpServletRequest, String, List) - Static method in class net.sourceforge.solexatools.util.PaginationUtil: subListSD.
submission - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
submissionComment - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
submissionDate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
submissionId - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
SubmissionSet - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionSet() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionSet
SubmissionType - Class in net.sourceforge.seqware.queryengine.webservice.model: A Submission type is used to describe an object that contains submission information, contacts for the submission, actions to be performed by the Archive, and file manifest.
SubmissionType() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
SubmissionType.ACTIONS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS
SubmissionType.ACTIONS.ACTION - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
SubmissionType.ACTIONS.ACTION.ADD - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.ADD() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.ADD
SubmissionType.ACTIONS.ACTION.HOLD - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.HOLD() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
SubmissionType.ACTIONS.ACTION.MODIFY - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.MODIFY() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
SubmissionType.ACTIONS.ACTION.RELEASE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.RELEASE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
SubmissionType.ACTIONS.ACTION.SUPPRESS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.SUPPRESS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
SubmissionType.ACTIONS.ACTION.VALIDATE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.ACTIONS.ACTION.VALIDATE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.VALIDATE
SubmissionType.CONTACTS - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.CONTACTS() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS
SubmissionType.CONTACTS.CONTACT - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.CONTACTS.CONTACT() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.CONTACTS.CONTACT
SubmissionType.FILES - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.FILES() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES
SubmissionType.FILES.FILE - Class in net.sourceforge.seqware.queryengine.webservice.model: Java class for anonymous complex type.
SubmissionType.FILES.FILE() - Constructor for class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.FILES.FILE
SUBMITTED - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant SUBMITTED="submitted"
SUCCESS - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant SUCCESS="success"
SUCCESS - Static variable in class net.sourceforge.seqware.common.module.ReturnValue: Constant SUCCESS=0
SUCCESS - Static variable in class net.sourceforge.seqware.pipeline.decider.Decider: Constant SUCCESS="success"
SUCCESS - Static variable in class net.sourceforge.seqware.pipeline.plugin.Plugin: Constant SUCCESS="success"
sum - Variable in class net.sourceforge.seqware.queryengine.backend.model.Coverage
SummaryData - Class in net.sourceforge.solexatools.util: SummaryData class.
SummaryData() - Constructor for class net.sourceforge.solexatools.util.SummaryData: Constructor for SummaryData.
SummaryLaunchWorkflowController - Class in net.sourceforge.solexatools.webapp.controller: SummaryLaunchWorkflowController class.
SummaryLaunchWorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Constructor for SummaryLaunchWorkflowController.
SummaryLaunchWorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.SummaryLaunchWorkflowController: Constructor for SummaryLaunchWorkflowController.
SummaryLine - Class in net.sourceforge.solexatools.util: SummaryLine class.
SummaryLine() - Constructor for class net.sourceforge.solexatools.util.SummaryLine: Constructor for SummaryLine.
supports(Class) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.LaneValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.LoginValidator: Returns true if this Validator supports the specified Class, and false otherwise.
supports(Class) - Method in class net.sourceforge.solexatools.validation.SampleValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.StudyValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator
supports(Class) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator
suppress - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
SV - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV=4
SV_COMPLEX - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_COMPLEX=1
SV_DELETION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_DELETION=2
SV_DELETION_AND_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_DELETION_AND_INVERSION=3
SV_DISPERSED_DUPLICATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_DISPERSED_DUPLICATION=4
SV_DUPLICATION_AND_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_DUPLICATION_AND_INVERSION=5
SV_INVERSION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_INVERSION=6
SV_LOCATION_DOWNSTREAM - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_LOCATION_DOWNSTREAM=2
SV_LOCATION_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_LOCATION_UNKNOWN=0
SV_LOCATION_UPSTREAM - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_LOCATION_UPSTREAM=1
SV_TANDEM_DUPLICATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_TANDEM_DUPLICATION=7
SV_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant SV_UNKNOWN=0
svType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
sw - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
SwBadFileException - Exception in net.sourceforge.seqware.common.err: Created by IntelliJ IDEA.
SwBadFileException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException: Constructor for SwBadFileException.
SwBadFileException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException: Constructor for SwBadFileException.
SwBadFileException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException: Constructor for SwBadFileException.
SwBadFileException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadFileException: Constructor for SwBadFileException.
SwBadModuleException - Exception in net.sourceforge.seqware.common.err: User: Xiaoshu Wang (xiao@renci.org) Date: 9/1/11 Time: 2:56 PM
SwBadModuleException() - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException: Constructor for SwBadModuleException.
SwBadModuleException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException: Constructor for SwBadModuleException.
SwBadModuleException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException: Constructor for SwBadModuleException.
SwBadModuleException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwBadModuleException: Constructor for SwBadModuleException.
SwParameterException - Exception in net.sourceforge.seqware.common.err: Created by IntelliJ IDEA.
SwParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException: Constructor for SwParameterException.
SwParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException: Constructor for SwParameterException.
SwParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException: Constructor for SwParameterException.
SwParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwParameterException: Constructor for SwParameterException.
SWQEFactory - Class in com.github.seqware.queryengine.factory: This is the SeqWare Query Engine factory and should be used as the primary entry-point for developers.
SWQEFactory() - Constructor for class com.github.seqware.queryengine.factory.SWQEFactory
SWQEFactory.Model_Type - Enum in com.github.seqware.queryengine.factory: ' These types describe different types of our model objects, for example the in memory objects load everything into memory.
SWQEFactory.Serialization_Type - Enum in com.github.seqware.queryengine.factory: These describe different types of serialization only
SWQEFactory.Storage_Type - Enum in com.github.seqware.queryengine.factory: These describe different types of our back-end, whether we store to files, to a database, or simply keep things in memory
SwRunnerParameterException - Exception in net.sourceforge.seqware.common.err: User: Xiaoshu Wang (xiao@renci.org) Date: 9/6/11 Time: 3:20 PM
SwRunnerParameterException() - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException: Constructor for SwRunnerParameterException.
SwRunnerParameterException(String) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException: Constructor for SwRunnerParameterException.
SwRunnerParameterException(String, Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException: Constructor for SwRunnerParameterException.
SwRunnerParameterException(Throwable) - Constructor for exception net.sourceforge.seqware.common.err.SwRunnerParameterException: Constructor for SwRunnerParameterException.
SymLinkFileReporter - Class in net.sourceforge.seqware.pipeline.plugins: SymLinkFileReporter class.
SymLinkFileReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.SymLinkFileReporter: Constructor for SymLinkFileReporter.

T

T__26 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant T__26=26
T__26 - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant T__26=26
table - Variable in class net.sourceforge.seqware.webservice.resources.tables.DatabaseResource
TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant TABLE_MODEL="tablemodel"
TABLE_MODEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant TABLE_MODEL="tablemodel"
TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.SequencerRunReportTableController: Constant TABLE_SEL="tablesel"
TABLE_SEL - Static variable in class net.sourceforge.solexatools.webapp.controller.StudyReportTableController: Constant TABLE_SEL="tablesel"
Tag - Class in com.github.seqware.queryengine.model: A Tag an instance of a TagSpec which contains all three of the values necessary for a GVF (ex: ID=ID_1 or Variant_seq=A,G or Reference_seq=G ).
TAG - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model: Constant TAG=10
Tag - Class in net.sourceforge.seqware.queryengine.backend.model: Tag class.
Tag() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Tag
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
tag - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
Tag.Builder - Class in com.github.seqware.queryengine.model
Tag.Builder() - Constructor for class com.github.seqware.queryengine.model.Tag.Builder
Tag.ValueType - Enum in com.github.seqware.queryengine.model
TAG_CHAR - Static variable in class com.github.seqware.queryengine.system.importers.OBOImporter: Constant TAG_CHAR='n'
TagAnnotationByPositionImporter - Class in net.sourceforge.seqware.queryengine.tools.importers: TagAnnotationByPositionImporter class.
TagAnnotationByPositionImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationByPositionImporter
TagAnnotationImporter - Class in net.sourceforge.seqware.queryengine.tools.importers: TagAnnotationImporter class.
TagAnnotationImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.TagAnnotationImporter
TagComparator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators: TagComparator class.
TagComparator() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.comparators.TagComparator
TagDumper - Class in net.sourceforge.seqware.queryengine.tools.exporters: TagDumper class.
TagDumper() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.TagDumper
Taggable<T> - Interface in com.github.seqware.queryengine.model.interfaces: Interface for all classes that can be tagged.
Taggable.NestedLevel - Class in com.github.seqware.queryengine.model.interfaces: This class represents both the tags that may be present at a particular level of the nested hash structure as well as tags that may be further up
Taggable.NestedLevel() - Constructor for class com.github.seqware.queryengine.model.interfaces.Taggable.NestedLevel
tagIndexTable - Variable in class net.sourceforge.seqware.queryengine.backend.store.impl.HBaseStore
TagIO - Class in com.github.seqware.queryengine.impl.protobufIO: TagIO class.
TagIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagIO
TagKeyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators: TagKeyCreator class.
TagKeyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyCreator: Constructor for TagKeyCreator.
TagKeyOnlyCreator - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators: TagKeyOnlyCreator class.
TagKeyOnlyCreator(TupleBinding) - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.keycreators.TagKeyOnlyCreator: Constructor for TagKeyOnlyCreator.
TagResource - Class in net.sourceforge.seqware.queryengine.webservice.view: TagResource class.
TagResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.TagResource
tags - Variable in class net.sourceforge.seqware.queryengine.backend.model.Model
tags - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
TAGS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
TAGS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
TagSet - Interface in com.github.seqware.queryengine.model: A set of Tag specifications
TagSet.Builder - Class in com.github.seqware.queryengine.model
TagSet.Builder() - Constructor for class com.github.seqware.queryengine.model.TagSet.Builder
TAGSET_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
TagSetCreator - Class in com.github.seqware.queryengine.system: Quick and dirty TagSet creator.
TagSetCreator() - Constructor for class com.github.seqware.queryengine.system.TagSetCreator: Constructor for TagSetCreator.
tagSetIDs - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
TagSetIO - Class in com.github.seqware.queryengine.impl.protobufIO: TagSetIO class.
TagSetIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagSetIO
TAGSETS_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant TAGSETS_PARAM='s'
TAGSPECIDS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
TagSpecIO - Class in com.github.seqware.queryengine.impl.protobufIO: TagSpecIO class.
TagSpecIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.TagSpecIO
TagTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders: TagTB class.
TagTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.TagTB
TagUtils - Class in net.sourceforge.solexatools.util: TagUtils class.
TagUtils() - Constructor for class net.sourceforge.solexatools.util.TagUtils
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.HOLD
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.MODIFY
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.RELEASE
target - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION.SUPPRESS
taxonid - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLENAME
temp - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
templateFile - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
TemplateResource - Class in net.sourceforge.seqware.queryengine.webservice.view: TemplateResource class.
TemplateResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.TemplateResource
test() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: test.
test() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: test.
test() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: test.
test(String[]) - Method in class net.sourceforge.seqware.pipeline.tools.ReportTest: test.
TEST_TABLE_PREFIX - Static variable in class com.github.seqware.queryengine.impl.HBaseStorage: Constant TEST_TABLE_PREFIX="Constants.Term.NAMESPACE.getTermValue(S"{trunked}
testBundle(File, File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: testBundle.
testBundle(File, File, String, String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: A bundle test occurs without metadata writeback
TestDatabaseCreator - Class in net.sourceforge.seqware.metadb.util: TestDatabaseCreator class.
TestDatabaseCreator() - Constructor for class net.sourceforge.seqware.metadb.util.TestDatabaseCreator
testIfNull(Object) - Method in class net.sourceforge.seqware.common.hibernate.WorkflowRunReport: testIfNull.
testIfNull(Object) - Method in class net.sourceforge.seqware.webservice.resources.BasicResource: testIfNull.
testIfNull(Object) - Method in class net.sourceforge.seqware.webservice.resources.BasicRestlet: testIfNull.
TestModule - Class in net.sourceforge.seqware.pipeline.module: This is an empty module mainly for testing purpose.
TestModule() - Constructor for class net.sourceforge.seqware.pipeline.module.TestModule
TextDumper - Class in net.sourceforge.seqware.queryengine.tools.exporters: TextDumper class.
TextDumper() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.TextDumper
thickEnd - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
thickStart - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
three_param_predicate() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: three_param_predicate.
TIMESTAMP_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType
title - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType
tList - Variable in class net.sourceforge.seqware.common.model.lists.ExperimentList
tList - Variable in class net.sourceforge.seqware.common.model.lists.FileList
tList - Variable in class net.sourceforge.seqware.common.model.lists.IUSList
tList - Variable in class net.sourceforge.seqware.common.model.lists.LaneList
tList - Variable in class net.sourceforge.seqware.common.model.lists.LibrarySelectionList
tList - Variable in class net.sourceforge.seqware.common.model.lists.LibrarySourceList
tList - Variable in class net.sourceforge.seqware.common.model.lists.LibraryStrategyList
tList - Variable in class net.sourceforge.seqware.common.model.lists.OrganismList
tList - Variable in class net.sourceforge.seqware.common.model.lists.PlatformList
tList - Variable in class net.sourceforge.seqware.common.model.lists.ProcessingList
tList - Variable in class net.sourceforge.seqware.common.model.lists.ReturnValueList
tList - Variable in class net.sourceforge.seqware.common.model.lists.SampleList
tList - Variable in class net.sourceforge.seqware.common.model.lists.SequencerRunList
tList - Variable in class net.sourceforge.seqware.common.model.lists.StudyList
tList - Variable in class net.sourceforge.seqware.common.model.lists.StudyTypeList
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowList
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamList
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList
tList - Variable in class net.sourceforge.seqware.common.model.lists.WorkflowRunList2
TmpFileStorage - Class in com.github.seqware.queryengine.impl: Stores objects in the temporary directory of the disk
TmpFileStorage(SerializationInterface) - Constructor for class com.github.seqware.queryengine.impl.TmpFileStorage: Constructor for TmpFileStorage.
toBaseN(int, int) - Static method in class com.github.seqware.queryengine.kernel.Compression: Converts an integer into a string representation of certain base.
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
toBuilder() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
toBuilder() - Method in class com.github.seqware.queryengine.model.Analysis: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.AnalysisSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.Feature: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.FeatureSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.Group: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.FeatureList: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.hbasemrlazy.MRLazyFeatureSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryAnalysisSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryGroup: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryQueryFutureImpl: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReference: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryReferenceSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryTagSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.impl.lazy.LazyFeatureSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.interfaces.ACL: Create an ACL builder started with a copy of this
toBuilder() - Method in interface com.github.seqware.queryengine.model.interfaces.Buildable: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.Reference: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.ReferenceSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.Tag: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in interface com.github.seqware.queryengine.model.TagSet: Creates a new builder initialized with the fields of an existing object
toBuilder() - Method in class com.github.seqware.queryengine.model.User: Creates a new builder initialized with the fields of an existing object
tokenNames - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant tokenNames="new String[] {, , ,"{trunked}
TOMBSTONE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
toString() - Method in class com.github.seqware.queryengine.impl.SimpleModelManager.AtomStatePair
toString() - Method in class com.github.seqware.queryengine.model.impl.AtomImpl
toString() - Method in class com.github.seqware.queryengine.util.FSGID
toString() - Method in class com.github.seqware.queryengine.util.SGID
toString() - Method in class net.sourceforge.seqware.common.hibernate.SequencerRunReport.Row
toString() - Method in class net.sourceforge.seqware.common.model.Expense
toString() - Method in class net.sourceforge.seqware.common.model.Experiment
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentLibraryDesign: toString.
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesign: toString.
toString() - Method in class net.sourceforge.seqware.common.model.ExperimentSpotDesignReadSpec
toString() - Method in class net.sourceforge.seqware.common.model.File
toString() - Method in class net.sourceforge.seqware.common.model.FileType
toString() - Method in class net.sourceforge.seqware.common.model.Invoice
toString() - Method in class net.sourceforge.seqware.common.model.IUS
toString() - Method in class net.sourceforge.seqware.common.model.IUSAttribute
toString() - Method in class net.sourceforge.seqware.common.model.Lane
toString() - Method in class net.sourceforge.seqware.common.model.LaneAttribute
toString() - Method in class net.sourceforge.seqware.common.model.LibrarySelection
toString() - Method in class net.sourceforge.seqware.common.model.LibrarySource
toString() - Method in class net.sourceforge.seqware.common.model.LibraryStrategy
toString() - Method in class net.sourceforge.seqware.common.model.Organism
toString() - Method in class net.sourceforge.seqware.common.model.Platform
toString() - Method in class net.sourceforge.seqware.common.model.Processing
toString() - Method in class net.sourceforge.seqware.common.model.Project
toString() - Method in class net.sourceforge.seqware.common.model.Registration
toString() - Method in class net.sourceforge.seqware.common.model.Sample
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRun
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunAttribute
toString() - Method in class net.sourceforge.seqware.common.model.SequencerRunDTO
toString() - Method in class net.sourceforge.seqware.common.model.ShareStudy
toString() - Method in class net.sourceforge.seqware.common.model.ShareWorkflowRun
toString() - Method in class net.sourceforge.seqware.common.model.Study
toString() - Method in class net.sourceforge.seqware.common.model.StudyType
toString() - Method in class net.sourceforge.seqware.common.model.Workflow
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParam
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowParamValue
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRun
toString() - Method in class net.sourceforge.seqware.common.model.WorkflowRunParam: toString.
toString() - Method in class net.sourceforge.seqware.common.module.FileMetadata
toString() - Method in class net.sourceforge.seqware.common.module.ReturnValue
toString() - Method in class net.sourceforge.seqware.pipeline.plugins.filelinker.FileLinkerLine
toString() - Method in class net.sourceforge.seqware.pipeline.workflowV2.model.Command
toString(WorkflowRunReportRow, StringBuilder) - Method in class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource: toString.
totalDataBlocks - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType
totalReads - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
totalSpots - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.DATABLOCK
totalSteps - Variable in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
totalSteps - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
trace(Object) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.debug(Object).
trace(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.debug(Object,Throwable).
transcriptassembly - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
transcriptId - Variable in class net.sourceforge.seqware.queryengine.backend.model.Feature
transcriptsequencing - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISTYPE
translatedSequence - Variable in class net.sourceforge.seqware.queryengine.backend.model.Consequence
TRANSLOCATION - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant TRANSLOCATION=5
TRANSLOCATION_COMPLEX - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant TRANSLOCATION_COMPLEX=3
TRANSLOCATION_INTERCHR - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant TRANSLOCATION_INTERCHR=2
TRANSLOCATION_INTRACHR - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant TRANSLOCATION_INTRACHR=1
TRANSLOCATION_UNKNOWN - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant TRANSLOCATION_UNKNOWN=0
translocationDestinationContig - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
translocationDestinationStartPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
translocationDestinationStopPosition - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
translocationType - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
TreeNodeHtmlUtil - Class in net.sourceforge.solexatools.util: TreeNodeHtmlUtil class.
TreeNodeHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.TreeNodeHtmlUtil
TrimAdapter - Class in net.sourceforge.seqware.pipeline.modules.alignment: Trim adapter segment (and any following sequence) from reads.
TrimAdapter() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.TrimAdapter
TrimAllReads - Class in net.sourceforge.seqware.pipeline.modules.alignment: Trim all reads down to a user-defined length.
TrimAllReads() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.TrimAllReads
TrimCountAdapter - Class in net.sourceforge.seqware.pipeline.modules.alignment: Trim adapter segment (and any following sequence) from reads, and get count & % of reads that contain adapter segment.
TrimCountAdapter() - Constructor for class net.sourceforge.seqware.pipeline.modules.alignment.TrimCountAdapter
TTLable - Interface in com.github.seqware.queryengine.model.interfaces: Interface for object that can be set to expire at some point in the future.
two_param_predicate() - Method in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: two_param_predicate.
type - Variable in class com.github.seqware.queryengine.util.LazyReference
type - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant
TYPE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.SequencerRunHtmlUtil: Constant TYPE_TREE="sr"
TYPE_TREE - Static variable in class net.sourceforge.solexatools.util.StudyHtmlUtil: Constant TYPE_TREE="st"
TYPE_TREE_COMPLETED - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil: Constant TYPE_TREE_COMPLETED="wfr"
TYPE_TREE_RUNNNING - Static variable in class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil: Constant TYPE_TREE_RUNNNING="wfrr"

U

U87LargeDeletionVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: U87LargeDeletionVariantImportWorker class.
U87LargeDeletionVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.U87LargeDeletionVariantImportWorker: Constructor for U87LargeDeletionVariantImportWorker.
U87TranslocationVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: U87TranslocationVariantImportWorker class.
U87TranslocationVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.U87TranslocationVariantImportWorker: Constructor for U87TranslocationVariantImportWorker.
unBindSessionFromTheThread() - Static method in class net.sourceforge.seqware.common.hibernate.InSessionExecutions: unBindSessionFromTheThread.
UNCKerberos - Class in net.sourceforge.solexatools.authentication: UNCKerberos class.
UNCKerberos() - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos
UNCKerberos.NamePasswordCallbackHandler - Class in net.sourceforge.solexatools.authentication
UNCKerberos.NamePasswordCallbackHandler(String, String) - Constructor for class net.sourceforge.solexatools.authentication.UNCKerberos.NamePasswordCallbackHandler
Unclassified - Static variable in class net.sourceforge.seqware.common.err.SeqwareExitCode: Constant Unclassified=1
uniqRead - Class in net.sourceforge.seqware.pipeline.modules.qc: Performing per lane based statistics Underlying script: sw_module_readDepth.pl Necessary programs: perl Expected output: read_depth.txt
uniqRead() - Constructor for class net.sourceforge.seqware.pipeline.modules.qc.uniqRead
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
units - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
UNKNOWN - Static variable in class net.sourceforge.seqware.common.metadata.Metadata: Constant UNKNOWN="unknown"
UNKNOWN_TYPE - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant UNKNOWN_TYPE=0
UNKNOWN_VALUE - Static variable in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
UNKNOWN_ZYGOSITY - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Variant: Constant UNKNOWN_ZYGOSITY=0
unmarshal(FileList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
unmarshal(IUSList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
unmarshal(LaneList) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
unmarshal(String) - Method in class net.sourceforge.seqware.common.model.adapters.XmlizeXML
unMarshal(T, Reader) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject: Turn an XML stream into an object, if possible.
unMarshal(Document, T) - Method in class net.sourceforge.seqware.common.util.xmltools.JaxbObject: Turn an XML stream into an object, if possible.
unMarshal(JaxbObject, Object, String) - Static method in class net.sourceforge.seqware.common.util.xmltools.XmlTools: unMarshal.
unpackageBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: unpackageBundle.
unpackageBundleFromS3(String) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: unpackageBundleFromS3.
unpackArchive(File, File, HttpServletRequest) - Static method in class net.sourceforge.solexatools.util.ZipFileUtil: Unpack a zip file
UnZip - Class in net.sourceforge.seqware.pipeline.tools: UnZip class.
UnZip() - Constructor for class net.sourceforge.seqware.pipeline.tools.UnZip
unzipFile(File, File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: FIXME: should make this optional to keep the original file
unzipFileOld(File, File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: FIXME: should make this optional to keep the original file
unzipPkg(String) - Static method in class net.sourceforge.seqware.pipeline.runner.Runner: FIXME: this needs to be migrated to something that is ZIP64 aware.
update(Atom...) - Method in interface com.github.seqware.queryengine.impl.BackEndInterface: Crawl through obj and update changes in the back-end.
update(Atom...) - Method in class com.github.seqware.queryengine.impl.SimplePersistentBackEnd: Crawl through obj and update changes in the back-end.
update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: update.
update(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: update.
update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: update.
update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: update.
update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService: update.
update(Integer, FileAttribute) - Method in interface net.sourceforge.seqware.common.business.FileAttributeService: update.
update(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService: update.
update(File) - Method in interface net.sourceforge.seqware.common.business.FileService: update.
update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: update.
update(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: update.
update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: update.
update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: update.
update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl: update.
update(Integer, FileAttribute) - Method in class net.sourceforge.seqware.common.business.impl.FileAttributeServiceImpl: update.
update(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: update.
update(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: update.
update(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: update.
update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: update.
update(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: update.
update(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: update.
update(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: update.
update(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: update.
update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl: update.
update(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl: update.
update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl: update.
update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl: update.
update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl: update.
update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl: update.
update(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: update.
update(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: update.
update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl: update.
update(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: update.
update(RegistrationDTO) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: update.
update(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: update.
update(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: update.
update(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: update.
update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: update.
update(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: update.
update(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: update.
update(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: update.
update(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: update.
update(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: update.
update(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: update.
update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: update.
update(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: update.
update(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: update.
update(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: update.
update(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: update.
update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: update.
update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: update.
update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: update.
update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: update.
update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: update.
update(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: update.
update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: update.
update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: update.
update(Registration, WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: update.
update(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: update.
update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: update.
update(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: update.
update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: update.
update(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService: update.
update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService: update.
update(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService: update.
update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService: update.
update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService: update.
update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService: update.
update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService: update.
update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService: update.
update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService: update.
update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService: update.
update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: update.
update(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: update.
update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService: update.
update(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService: update.
update(RegistrationDTO) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: update.
update(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService: update.
update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService: update.
update(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: update.
update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: update.
update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: update.
update(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: update.
update(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: update.
update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: update.
update(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: update.
update(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: update.
update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: update.
update(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: update.
update(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: update.
update(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: update.
update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: update.
update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: update.
update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: update.
update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: update.
update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: update.
update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: update.
update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: update.
update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: update.
update(Registration, WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: update.
update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: update.
update(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: update.
update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: update.
update(ExperimentAttribute) - Method in interface net.sourceforge.seqware.common.dao.ExperimentAttributeDAO: update.
update(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: update.
update(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: update.
update(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO: update.
update(ExperimentLink) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLinkDAO: update.
update(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO: update.
update(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO: update.
update(FileAttribute) - Method in interface net.sourceforge.seqware.common.dao.FileAttributeDAO: update.
update(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: update.
update(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: update.
update(ExperimentAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentAttributeDAOHibernate: update.
update(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: update.
update(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: update.
update(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate: update.
update(ExperimentLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLinkDAOHibernate: update.
update(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate: update.
update(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate: update.
update(FileAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileAttributeDAOHibernate: update.
update(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: update.
update(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: update.
update(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: update.
update(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: update.
update(IUSAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSAttributeDAOHibernate: update.
update(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: update.
update(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: update.
update(IUSLink) - Method in interface net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAO: update.
update(IUSLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSLinkDAOHibernate: update.
update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAO: update.
update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneAttributeDAOHibernate: update.
update(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: update.
update(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: update.
update(LaneAttribute) - Method in interface net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAO: update.
update(LaneAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneLinkDAOHibernate: update.
update(ProcessingAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingAttributeDAOHibernate: update.
update(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: update.
update(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: update.
update(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate: update.
update(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate: update.
update(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate: update.
update(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate: update.
update(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate: update.
update(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate: update.
update(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate: update.
update(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: update.
update(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate: update.
update(SampleAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleAttributeDAOHibernate: update.
update(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: update.
update(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: update.
update(SampleLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleLinkDAOHibernate: update.
update(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: update.
update(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: update.
update(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: update.
update(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: update.
update(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: update.
update(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: update.
update(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: update.
update(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: update.
update(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: update.
update(StudyAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyAttributeDAOHibernate: update.
update(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: update.
update(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: update.
update(StudyLink) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyLinkDAOHibernate: update.
update(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: update.
update(WorkflowAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate: update.
update(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: update.
update(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: update.
update(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: update.
update(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: update.
update(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: update.
update(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: update.
update(WorkflowRunAttribute) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate: update.
update(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: update.
update(WorkflowRun, List<Integer>) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: update.
update(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: update.
update(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: update.
update(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: update.
update(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: update.
update(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: update.
update(IUSAttribute) - Method in interface net.sourceforge.seqware.common.dao.IUSAttributeDAO: update.
update(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: update.
update(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: update.
update(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: update.
update(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: update.
update(ProcessingAttribute) - Method in interface net.sourceforge.seqware.common.dao.ProcessingAttributeDAO: update.
update(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: update.
update(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: update.
update(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO: update.
update(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO: update.
update(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO: update.
update(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO: update.
update(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO: update.
update(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO: update.
update(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO: update.
update(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO: update.
update(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO: update.
update(SampleAttribute) - Method in interface net.sourceforge.seqware.common.dao.SampleAttributeDAO: update.
update(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: update.
update(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: update.
update(SampleLink) - Method in interface net.sourceforge.seqware.common.dao.SampleLinkDAO: update.
update(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: update.
update(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: update.
update(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: update.
update(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: update.
update(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: update.
update(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: update.
update(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: update.
update(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO: update.
update(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: update.
update(StudyAttribute) - Method in interface net.sourceforge.seqware.common.dao.StudyAttributeDAO: update.
update(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: update.
update(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: update.
update(StudyLink) - Method in interface net.sourceforge.seqware.common.dao.StudyLinkDAO: update.
update(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO: update.
update(WorkflowAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowAttributeDAO: update.
update(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: update.
update(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: update.
update(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: update.
update(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: update.
update(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: update.
update(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: update.
update(WorkflowRunAttribute) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunAttributeDAO: update.
update(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: update.
update(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: update.
update(WorkflowRun, List<Integer>) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: update.
update(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: update.
update(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: update.
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: update_processing_event.
update_processing_event(int, ReturnValue) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: update_processing_event.
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: update_processing_event.
update_processing_event(int, ReturnValue) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: update_processing_event.
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: update_processing_status.
update_processing_status(int, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: update_processing_status.
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: update_processing_status.
update_processing_status(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: update_processing_status.
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: update_processing_workflow_run.
update_processing_workflow_run(int, int) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: update_processing_workflow_run.
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: update_processing_workflow_run.
update_processing_workflow_run(int, int) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: update_processing_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: update_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: update_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: update_workflow_run.
update_workflow_run(int, String, String, String, String, String, String, String, String, int, int, String, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: update_workflow_run.
updateACL(ACL) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateACL.
updateAnalysisPlugin(AnalysisPlugin) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateAnalysisPlugin.
updateAnalysisSet(AnalysisSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateAnalysisSet.
updateAttribute(AttributeDto) - Method in interface net.sourceforge.seqware.webservice.resources.tables.FileAttributeResource: updateAttribute.
updateAttribute(AttributeDto) - Method in class net.sourceforge.seqware.webservice.resources.tables.FileAttributeServerResource: updateAttribute.
updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentLibraryDesignService: updateDetached.
updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: updateDetached.
updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.business.ExperimentService: updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignReadSpecService: updateDetached.
updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.business.ExperimentSpotDesignService: updateDetached.
updateDetached(File) - Method in interface net.sourceforge.seqware.common.business.FileService: updateDetached.
updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.business.FileService: updateDetached.
updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.business.FileTypeService: updateDetached.
updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentLibraryDesignServiceImpl: updateDetached.
updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: updateDetached.
updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentServiceImpl: updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignReadSpecServiceImpl: updateDetached.
updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.business.impl.ExperimentSpotDesignServiceImpl: updateDetached.
updateDetached(File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: updateDetached.
updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.business.impl.FileServiceImpl: updateDetached.
updateDetached(FileType) - Method in class net.sourceforge.seqware.common.business.impl.FileTypeServiceImpl: updateDetached.
updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: updateDetached.
updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.business.impl.InvoiceServiceImpl: updateDetached.
updateDetached(IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: updateDetached.
updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.business.impl.IUSServiceImpl: updateDetached.
updateDetached(Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: updateDetached.
updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: updateDetached.
updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySelectionServiceImpl: updateDetached.
updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.business.impl.LibrarySourceServiceImpl: updateDetached.
updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.business.impl.LibraryStrategyServiceImpl: updateDetached.
updateDetached(Organism) - Method in class net.sourceforge.seqware.common.business.impl.OrganismServiceImpl: updateDetached.
updateDetached(Platform) - Method in class net.sourceforge.seqware.common.business.impl.PlatformServiceImpl: updateDetached.
updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingExperimentsServiceImpl: updateDetached.
updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingIUSServiceImpl: updateDetached.
updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingLanesServiceImpl: updateDetached.
updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingRelationshipServiceImpl: updateDetached.
updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSamplesServiceImpl: updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingSequencerRunsServiceImpl: updateDetached.
updateDetached(Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: updateDetached.
updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingServiceImpl: updateDetached.
updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.business.impl.ProcessingStudiesServiceImpl: updateDetached.
updateDetached(Project) - Method in class net.sourceforge.seqware.common.business.impl.ProjectServiceImpl: updateDetached.
updateDetached(Registration) - Method in class net.sourceforge.seqware.common.business.impl.RegistrationServiceImpl: updateDetached.
updateDetached(Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: updateDetached.
updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.business.impl.SampleServiceImpl: updateDetached.
updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: updateDetached.
updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.business.impl.SequencerRunServiceImpl: updateDetached.
updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.business.impl.ShareExperimentServiceImpl: updateDetached.
updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.business.impl.ShareFileServiceImpl: updateDetached.
updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.business.impl.ShareLaneServiceImpl: updateDetached.
updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.business.impl.ShareProcessingServiceImpl: updateDetached.
updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.business.impl.ShareSampleServiceImpl: updateDetached.
updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.business.impl.ShareStudyServiceImpl: updateDetached.
updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.ShareWorkflowRunServiceImpl: updateDetached.
updateDetached(Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: updateDetached.
updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: updateDetached.
updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.business.impl.StudyTypeServiceImpl: updateDetached.
updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: updateDetached.
updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: updateDetached.
updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: updateDetached.
updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: updateDetached.
updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: updateDetached.
updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: updateDetached.
updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: updateDetached.
updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: updateDetached.
updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.business.InvoiceService: updateDetached.
updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService: updateDetached.
updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.business.IUSService: updateDetached.
updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService: updateDetached.
updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.business.LaneService: updateDetached.
updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.business.LibrarySelectionService: updateDetached.
updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.business.LibrarySourceService: updateDetached.
updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.business.LibraryStrategyService: updateDetached.
updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.business.OrganismService: updateDetached.
updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.business.PlatformService: updateDetached.
updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.business.ProcessingExperimentsService: updateDetached.
updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.business.ProcessingIUSService: updateDetached.
updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.business.ProcessingLanesService: updateDetached.
updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.business.ProcessingRelationshipService: updateDetached.
updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.business.ProcessingSamplesService: updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.business.ProcessingSequencerRunsService: updateDetached.
updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: updateDetached.
updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.business.ProcessingService: updateDetached.
updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.business.ProcessingStudiesService: updateDetached.
updateDetached(Project) - Method in interface net.sourceforge.seqware.common.business.ProjectService: updateDetached.
updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.business.RegistrationService: updateDetached.
updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService: updateDetached.
updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.business.SampleService: updateDetached.
updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: updateDetached.
updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.business.SequencerRunService: updateDetached.
updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.business.ShareExperimentService: updateDetached.
updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.business.ShareFileService: updateDetached.
updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.business.ShareLaneService: updateDetached.
updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.business.ShareProcessingService: updateDetached.
updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.business.ShareSampleService: updateDetached.
updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.business.ShareStudyService: updateDetached.
updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.business.ShareWorkflowRunService: updateDetached.
updateDetached(Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: updateDetached.
updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.business.StudyService: updateDetached.
updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.business.StudyTypeService: updateDetached.
updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: updateDetached.
updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamService: updateDetached.
updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.business.WorkflowParamValueService: updateDetached.
updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunParamService: updateDetached.
updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.business.WorkflowRunService: updateDetached.
updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: updateDetached.
updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.business.WorkflowService: updateDetached.
updateDetached(Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: updateDetached.
updateDetached(Registration, Experiment) - Method in interface net.sourceforge.seqware.common.dao.ExperimentDAO: updateDetached.
updateDetached(ExperimentLibraryDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentLibraryDesignDAO: updateDetached.
updateDetached(ExperimentSpotDesign) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignDAO: updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in interface net.sourceforge.seqware.common.dao.ExperimentSpotDesignReadSpecDAO: updateDetached.
updateDetached(File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: updateDetached.
updateDetached(Registration, File) - Method in interface net.sourceforge.seqware.common.dao.FileDAO: updateDetached.
updateDetached(FileType) - Method in interface net.sourceforge.seqware.common.dao.FileTypeDAO: updateDetached.
updateDetached(Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: updateDetached.
updateDetached(Registration, Experiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentDAOHibernate: updateDetached.
updateDetached(ExperimentLibraryDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentLibraryDesignDAOHibernate: updateDetached.
updateDetached(ExperimentSpotDesign) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignDAOHibernate: updateDetached.
updateDetached(ExperimentSpotDesignReadSpec) - Method in class net.sourceforge.seqware.common.dao.hibernate.ExperimentSpotDesignReadSpecDAOHibernate: updateDetached.
updateDetached(File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: updateDetached.
updateDetached(Registration, File) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileDAOHibernate: updateDetached.
updateDetached(FileType) - Method in class net.sourceforge.seqware.common.dao.hibernate.FileTypeDAOHibernate: updateDetached.
updateDetached(Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: updateDetached.
updateDetached(Registration, Invoice) - Method in class net.sourceforge.seqware.common.dao.hibernate.InvoiceDAOHibernate: updateDetached.
updateDetached(IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: updateDetached.
updateDetached(Registration, IUS) - Method in class net.sourceforge.seqware.common.dao.hibernate.IUSDAOHibernate: updateDetached.
updateDetached(Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: updateDetached.
updateDetached(Registration, Lane) - Method in class net.sourceforge.seqware.common.dao.hibernate.LaneDAOHibernate: updateDetached.
updateDetached(LibrarySelection) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySelectionDAOHibernate: updateDetached.
updateDetached(LibrarySource) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibrarySourceDAOHibernate: updateDetached.
updateDetached(LibraryStrategy) - Method in class net.sourceforge.seqware.common.dao.hibernate.LibraryStrategyDAOHibernate: updateDetached.
updateDetached(Organism) - Method in class net.sourceforge.seqware.common.dao.hibernate.OrganismDAOHibernate: updateDetached.
updateDetached(Platform) - Method in class net.sourceforge.seqware.common.dao.hibernate.PlatformDAOHibernate: updateDetached.
updateDetached(Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: updateDetached.
updateDetached(Registration, Processing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingDAOHibernate: updateDetached.
updateDetached(ProcessingExperiments) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingExperimentsDAOHibernate: updateDetached.
updateDetached(ProcessingIus) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingIUSDAOHibernate: updateDetached.
updateDetached(ProcessingLanes) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingLanesDAOHibernate: updateDetached.
updateDetached(ProcessingRelationship) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingRelationshipDAOHibernate: updateDetached.
updateDetached(ProcessingSamples) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSamplesDAOHibernate: updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingSequencerRunsDAOHibernate: updateDetached.
updateDetached(ProcessingStudies) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProcessingStudiesDAOHibernate: updateDetached.
updateDetached(Project) - Method in class net.sourceforge.seqware.common.dao.hibernate.ProjectDAOHibernate: updateDetached.
updateDetached(Registration) - Method in class net.sourceforge.seqware.common.dao.hibernate.RegistrationDAOHibernate: updateDetached.
updateDetached(Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: updateDetached.
updateDetached(Registration, Sample) - Method in class net.sourceforge.seqware.common.dao.hibernate.SampleDAOHibernate: updateDetached.
updateDetached(SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: updateDetached.
updateDetached(Registration, SequencerRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.SequencerRunDAOHibernate: updateDetached.
updateDetached(ShareExperiment) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareExperimentDAOHibernate: updateDetached.
updateDetached(ShareFile) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareFileDAOHibernate: updateDetached.
updateDetached(ShareLane) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareLaneDAOHibernate: updateDetached.
updateDetached(ShareProcessing) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareProcessingDAOHibernate: updateDetached.
updateDetached(ShareSample) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareSampleDAOHibernate: updateDetached.
updateDetached(ShareStudy) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareStudyDAOHibernate: updateDetached.
updateDetached(ShareWorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.ShareWorkflowRunDAOHibernate: updateDetached.
updateDetached(Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: updateDetached.
updateDetached(Registration, Study) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: updateDetached.
updateDetached(StudyType) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyTypeDAOHibernate: updateDetached.
updateDetached(Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: updateDetached.
updateDetached(Registration, Workflow) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: updateDetached.
updateDetached(WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: updateDetached.
updateDetached(Registration, WorkflowParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: updateDetached.
updateDetached(WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: updateDetached.
updateDetached(WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: updateDetached.
updateDetached(Registration, WorkflowRun) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: updateDetached.
updateDetached(WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: updateDetached.
updateDetached(Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: updateDetached.
updateDetached(Registration, Invoice) - Method in interface net.sourceforge.seqware.common.dao.InvoiceDAO: updateDetached.
updateDetached(IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: updateDetached.
updateDetached(Registration, IUS) - Method in interface net.sourceforge.seqware.common.dao.IUSDAO: updateDetached.
updateDetached(Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: updateDetached.
updateDetached(Registration, Lane) - Method in interface net.sourceforge.seqware.common.dao.LaneDAO: updateDetached.
updateDetached(LibrarySelection) - Method in interface net.sourceforge.seqware.common.dao.LibrarySelectionDAO: updateDetached.
updateDetached(LibrarySource) - Method in interface net.sourceforge.seqware.common.dao.LibrarySourceDAO: updateDetached.
updateDetached(LibraryStrategy) - Method in interface net.sourceforge.seqware.common.dao.LibraryStrategyDAO: updateDetached.
updateDetached(Organism) - Method in interface net.sourceforge.seqware.common.dao.OrganismDAO: updateDetached.
updateDetached(Platform) - Method in interface net.sourceforge.seqware.common.dao.PlatformDAO: updateDetached.
updateDetached(Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: updateDetached.
updateDetached(Registration, Processing) - Method in interface net.sourceforge.seqware.common.dao.ProcessingDAO: updateDetached.
updateDetached(ProcessingExperiments) - Method in interface net.sourceforge.seqware.common.dao.ProcessingExperimentsDAO: updateDetached.
updateDetached(ProcessingIus) - Method in interface net.sourceforge.seqware.common.dao.ProcessingIUSDAO: updateDetached.
updateDetached(ProcessingLanes) - Method in interface net.sourceforge.seqware.common.dao.ProcessingLanesDAO: updateDetached.
updateDetached(ProcessingRelationship) - Method in interface net.sourceforge.seqware.common.dao.ProcessingRelationshipDAO: updateDetached.
updateDetached(ProcessingSamples) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSamplesDAO: updateDetached.
updateDetached(ProcessingSequencerRuns) - Method in interface net.sourceforge.seqware.common.dao.ProcessingSequencerRunsDAO: updateDetached.
updateDetached(ProcessingStudies) - Method in interface net.sourceforge.seqware.common.dao.ProcessingStudiesDAO: updateDetached.
updateDetached(Project) - Method in interface net.sourceforge.seqware.common.dao.ProjectDAO: updateDetached.
updateDetached(Registration) - Method in interface net.sourceforge.seqware.common.dao.RegistrationDAO: updateDetached.
updateDetached(Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: updateDetached.
updateDetached(Registration, Sample) - Method in interface net.sourceforge.seqware.common.dao.SampleDAO: updateDetached.
updateDetached(SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: updateDetached.
updateDetached(Registration, SequencerRun) - Method in interface net.sourceforge.seqware.common.dao.SequencerRunDAO: updateDetached.
updateDetached(ShareExperiment) - Method in interface net.sourceforge.seqware.common.dao.ShareExperimentDAO: updateDetached.
updateDetached(ShareFile) - Method in interface net.sourceforge.seqware.common.dao.ShareFileDAO: updateDetached.
updateDetached(ShareLane) - Method in interface net.sourceforge.seqware.common.dao.ShareLaneDAO: updateDetached.
updateDetached(ShareProcessing) - Method in interface net.sourceforge.seqware.common.dao.ShareProcessingDAO: updateDetached.
updateDetached(ShareSample) - Method in interface net.sourceforge.seqware.common.dao.ShareSampleDAO: updateDetached.
updateDetached(ShareStudy) - Method in interface net.sourceforge.seqware.common.dao.ShareStudyDAO: updateDetached.
updateDetached(ShareWorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.ShareWorkflowRunDAO: updateDetached.
updateDetached(Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: updateDetached.
updateDetached(Registration, Study) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: updateDetached.
updateDetached(StudyType) - Method in interface net.sourceforge.seqware.common.dao.StudyTypeDAO: updateDetached.
updateDetached(Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: updateDetached.
updateDetached(Registration, Workflow) - Method in interface net.sourceforge.seqware.common.dao.WorkflowDAO: updateDetached.
updateDetached(WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: updateDetached.
updateDetached(Registration, WorkflowParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamDAO: updateDetached.
updateDetached(WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: updateDetached.
updateDetached(Registration, WorkflowParamValue) - Method in interface net.sourceforge.seqware.common.dao.WorkflowParamValueDAO: updateDetached.
updateDetached(WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: updateDetached.
updateDetached(Registration, WorkflowRun) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunDAO: updateDetached.
updateDetached(WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: updateDetached.
updateDetached(Registration, WorkflowRunParam) - Method in interface net.sourceforge.seqware.common.dao.WorkflowRunParamDAO: updateDetached.
updateFeature(Feature) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateFeature.
updateFeatureSet(FeatureSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateFeatureSet.
updateGroup(Group) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateGroup.
updateLane(Sample, MultipartFile, MultipartFile, String, String, Registration) - Method in class net.sourceforge.seqware.common.business.impl.LaneServiceImpl: updateLane.
updateOwners(Integer) - Method in class net.sourceforge.seqware.common.business.impl.StudyServiceImpl: updateOwners.
updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.business.StudyService: updateOwners.
updateOwners(Integer) - Method in class net.sourceforge.seqware.common.dao.hibernate.StudyDAOHibernate: updateOwners.
updateOwners(Integer) - Method in interface net.sourceforge.seqware.common.dao.StudyDAO: updateOwners.
updateReference(Reference) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateReference.
updateReferenceSet(ReferenceSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateReferenceSet.
updateSelectedIds(HttpServletRequest, String, boolean, List<String>) - Static method in class net.sourceforge.solexatools.util.BulkUtil: updateSelectedIds.
updateTag(Tag) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateTag.
updateTagSet(TagSet) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateTagSet.
updateUser(User) - Method in interface net.sourceforge.seqware.queryengine.backend.store.FeatureStoreInterface: updateUser.
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataDB: updateWorkflow.
updateWorkflow(int, String) - Method in interface net.sourceforge.seqware.common.metadata.MetadataInterface: updateWorkflow.
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataNoConnection: updateWorkflow.
updateWorkflow(int, String) - Method in class net.sourceforge.seqware.common.metadata.MetadataWS: updateWorkflow.
updateWorkflowRun(int, String, String, String, String, String, String) - Method in class net.sourceforge.seqware.queryengine.webservice.model.MetadataDB: updateWorkflowRun.
updateWorkflowRun(WorkflowRun) - Method in class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource: updateWorkflowRun.
upgradeFeatureSGID(Feature) - Method in class com.github.seqware.queryengine.model.impl.inMemory.InMemoryFeatureSet: upgradeFeatureSGID.
uploadFile(Study, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService: uploadFile.
uploadFile(Experiment, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService: uploadFile.
uploadFile(Sample, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService: uploadFile.
uploadFile(Lane, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService: uploadFile.
uploadFile(IUS, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService: uploadFile.
uploadFile(Processing, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService: uploadFile.
uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in interface net.sourceforge.seqware.common.business.FileUploadService: uploadFile.
uploadFile(Study, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: uploadFile.
uploadFile(Experiment, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: uploadFile.
uploadFile(Sample, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: uploadFile.
uploadFile(Lane, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: uploadFile.
uploadFile(IUS, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: uploadFile.
uploadFile(Processing, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: uploadFile.
uploadFile(SequencerRun, UploadFile, FileType, Registration) - Method in class net.sourceforge.seqware.common.business.impl.FileUploadServiceImpl: uploadFile.
UploadFile - Class in net.sourceforge.seqware.common.business: UploadFile class.
UploadFile() - Constructor for class net.sourceforge.seqware.common.business.UploadFile: Constructor for UploadFile.
UploadFileController - Class in net.sourceforge.solexatools.webapp.controller: UploadFileController class.
UploadFileController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController: Constructor for UploadFileController.
UploadFileController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileController: Constructor for UploadFileController.
UploadFileSetupController - Class in net.sourceforge.solexatools.webapp.controller: UploadFileSetupController class.
UploadFileSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadFileSetupController: Constructor for UploadFileSetupController.
UploadFileValidator - Class in net.sourceforge.solexatools.validation: UploadFileValidator class.
UploadFileValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadFileValidator: Constructor for UploadFileValidator.
UploadSequence - Class in net.sourceforge.seqware.common.model
UploadSequence() - Constructor for class net.sourceforge.seqware.common.model.UploadSequence: Constructor for UploadSequence.
UploadSequenceController - Class in net.sourceforge.solexatools.webapp.controller: UploadSequenceController class.
UploadSequenceController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Constructor for UploadSequenceController.
UploadSequenceController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceController: Constructor for UploadSequenceController.
UploadSequenceSetupController - Class in net.sourceforge.solexatools.webapp.controller: UploadSequenceSetupController class.
UploadSequenceSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.UploadSequenceSetupController: Constructor for UploadSequenceSetupController.
UploadSequenceValidator - Class in net.sourceforge.solexatools.validation: UploadSequenceValidator class.
UploadSequenceValidator() - Constructor for class net.sourceforge.solexatools.validation.UploadSequenceValidator: Constructor for UploadSequenceValidator.
url - Variable in class net.sourceforge.seqware.common.module.ReturnValue
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK.URLLINK
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK.URLLINK
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK.URLLINK
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK.URLLINK
url - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK.URLLINK
urlLabel - Variable in class net.sourceforge.seqware.common.module.ReturnValue
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTLINKS.EXPERIMENTLINK
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNLINKS.RUNLINK
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLELINKS.SAMPLELINK
urllink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYLINKS.STUDYLINK
urlString - Variable in class net.sourceforge.seqware.queryengine.webservice.view.GenericTemplateResource
User - Class in com.github.seqware.queryengine.model: A user of the Generic Feature Store.
User.Builder - Class in com.github.seqware.queryengine.model
User.Builder() - Constructor for class com.github.seqware.queryengine.model.User.Builder
USER_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
UserIO - Class in com.github.seqware.queryengine.impl.protobufIO: UserIO class.
UserIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.UserIO
USERS_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
UtilIO - Class in com.github.seqware.queryengine.impl.protobufIO: UtilIO class.
UtilIO() - Constructor for class com.github.seqware.queryengine.impl.protobufIO.UtilIO
Utility - Class in com.github.seqware.queryengine.system: Utility procedures for interacting outside the API
Utility() - Constructor for class com.github.seqware.queryengine.system.Utility

V

Validate - Class in net.sourceforge.seqware.common.util.filetools.validate: Validate class.
Validate() - Constructor for class net.sourceforge.seqware.common.util.filetools.validate.Validate
validate - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SubmissionType.ACTIONS.ACTION
validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileLinkReportResource: validate.
validate() - Method in class net.sourceforge.seqware.webservice.resources.tables.FileReverseHierarchyDisplayResource: validate.
validate(String) - Method in class net.sourceforge.solexatools.util.HTMLTagValidator: validate.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.FileValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowParamValidator: Validates the specified Object.
validate(Object, Errors) - Method in class net.sourceforge.solexatools.validation.WorkflowValidator: Validates the specified Object.
validateBundle(File) - Method in class net.sourceforge.seqware.pipeline.bundle.Bundle: validateBundle.
validateEmail(String, String, Errors) - Method in class net.sourceforge.solexatools.validation.LoginValidator: Validates an email address.
validateEmailAddressesMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator: Determines if the registration's email address and confirm email address match.
validateEmailNotInUse(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator: validateEmailNotInUse.
validateExists(MultipartFile, String, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: validateExists.
validateExpectedNumberReads(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator: validateExpectedNumberReads.
validateExpectedNumberReads(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator: validateExpectedNumberReads.
validateExpectedNumberRuns(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator: validateExpectedNumberRuns.
validateExpectedNumberRuns(Sample, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator: validateExpectedNumberRuns.
validateExtension(String, String, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: validateExtension.
validateExtension(MultipartFile, MultipartFile, Integer, Errors) - Method in class net.sourceforge.solexatools.validation.UploadSequenceValidator
validateInvitationCode(String, Errors) - Method in class net.sourceforge.solexatools.validation.RegistrationValidator: validateInvitationCode.
validateLaneCount(SequencerRunWizardDTO, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunWizardValidator: validateLaneCount.
validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.LaneValidator: Determines if the Lane's email address and confirm email address match.
validateName(String, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator: Determines if the experiment's email address and confirm email address match.
validatePasswordsMatch(String, String, Errors) - Static method in class net.sourceforge.solexatools.validation.RegistrationValidator: Determines if the registration's password and confirm password match.
validateProtocol(String, String[], Errors) - Method in class net.sourceforge.solexatools.validation.UploadFileValidator: validateProtocol.
validateRefLane(SequencerRun, Errors) - Method in class net.sourceforge.solexatools.validation.SequencerRunValidator: validateRefLane.
validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentUpdateValidator
validateTitle(Experiment, Errors) - Method in class net.sourceforge.solexatools.validation.ExperimentValidator: Determines if the experiment's email address and confirm email address match.
validateTitle(String, Errors) - Method in class net.sourceforge.solexatools.validation.SampleValidator: Determines if the sample's email address and confirm email address match.
validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyUpdateValidator
validateTitle(Study, Errors) - Method in class net.sourceforge.solexatools.validation.StudyValidator: Determines if the experiment's email address and confirm email address match.
ValidationReportService - Interface in net.sourceforge.seqware.common.business: A collection of reports useful when verifying that data in the SeqWare meta db is correct.
ValidationReportServiceImpl - Class in net.sourceforge.seqware.common.business.impl
ValidationReportServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl
ValidationReportServiceImpl.ReportEntry - Class in net.sourceforge.seqware.common.business.impl
ValidationReportServiceImpl.ReportEntry() - Constructor for class net.sourceforge.seqware.common.business.impl.ValidationReportServiceImpl.ReportEntry
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISATTRIBUTES.ANALYSISATTRIBUTE
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.EXPERIMENTATTRIBUTES.EXPERIMENTATTRIBUTE
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.ExperimentType.PLATFORM.ABISOLID.COLORMATRIX.COLOR
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.RunType.RUNATTRIBUTES.RUNATTRIBUTE
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.SampleType.SAMPLEATTRIBUTES.SAMPLEATTRIBUTE
value - Variable in class net.sourceforge.seqware.queryengine.webservice.model.StudyType.STUDYATTRIBUTES.STUDYATTRIBUTE
VALUE_SEPARATOR_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant VALUE_SEPARATOR_PARAM=','
valueOf(String) - Static method in enum com.github.seqware.queryengine.Constants.Term: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB: Returns the enum constant of this type with the specified name.
valueOf(int) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
valueOf(Descriptors.EnumValueDescriptor) - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.CreateUpdateManager.State: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Model_Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Serialization_Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Storage_Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.kernel.RPNStack.Operation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Feature.AdditionalAttributeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Feature.Strand: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.QueryInterface.Location: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.github.seqware.queryengine.model.Tag.ValueType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Requirement.Type: Returns the enum constant of this type with the specified name.
values() - Static method in enum com.github.seqware.queryengine.Constants.Term: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.dto.QueryEngine.FeaturePB.StrandPB: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.CreateUpdateManager.State: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Model_Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Serialization_Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.factory.SWQEFactory.Storage_Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.kernel.RPNStack.Operation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Feature.AdditionalAttributeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Feature.Strand: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.QueryInterface.Location: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.github.seqware.queryengine.model.Tag.ValueType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.common.hibernate.FindAllTheFiles.Header: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.common.module.ReturnValue.ExitStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.module.ModuleMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflow.BasicWorkflow.Job: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Module: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sourceforge.seqware.pipeline.workflowV2.model.Requirement.Type: Returns an array containing the constants of this enum type, in the order they are declared.
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBaseBatchedPlugin: This should be overridden with the result.
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: This should be overridden with the result.
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRFeatureSetCountPlugin: This should be overridden with the result.
variableResult() - Method in class com.github.seqware.queryengine.plugins.hbasemr.MRVCFDumperPlugin: This should be overridden with the result.
Variant - Class in net.sourceforge.seqware.queryengine.backend.model: Variant class.
Variant() - Constructor for class net.sourceforge.seqware.queryengine.backend.model.Variant
VariantConsequenceByPositionImporter - Class in net.sourceforge.seqware.queryengine.tools.importers: VariantConsequenceByPositionImporter class.
VariantConsequenceByPositionImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceByPositionImporter
VariantConsequenceImporter - Class in net.sourceforge.seqware.queryengine.tools.importers: VariantConsequenceImporter class.
VariantConsequenceImporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantConsequenceImporter
VariantImporter - Class in net.sourceforge.seqware.queryengine.tools.importers: VariantImporter class.
VariantImporter(int) - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.VariantImporter: Constructor for VariantImporter.
VariantIteratorProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators: VariantIteratorProcessor class.
VariantIteratorProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.VariantIteratorProcessor
VariantProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors: VariantProcessor class.
VariantProcessor(String, Store, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Constructor for VariantProcessor.
VariantProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantProcessor: Constructor for VariantProcessor.
VariantStatsProcessor - Class in net.sourceforge.seqware.queryengine.tools.iterators.processors: VariantStatsProcessor class.
VariantStatsProcessor(String, BerkeleyDBStore, boolean, boolean, int, int, int, int, int, int) - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor: Constructor for VariantStatsProcessor.
VariantStatsProcessor() - Constructor for class net.sourceforge.seqware.queryengine.tools.iterators.processors.VariantStatsProcessor: Constructor for VariantStatsProcessor.
VariantTB - Class in net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders: VariantTB class.
VariantTB() - Constructor for class net.sourceforge.seqware.queryengine.backend.io.berkeleydb.tuplebinders.VariantTB
VARIENT - Static variable in class net.sourceforge.seqware.queryengine.backend.model.Model: Constant VARIENT=0
VBYTES_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
VCF - Static variable in class com.github.seqware.queryengine.system.exporters.VCFDumper: Constant VCF="VCFVariantImportWorker.VCF"
VCF - Static variable in class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker: Constant VCF="VCF"
VCF_CALLED_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_CALLED_BASE="call_base"
VCF_CONSENSUS_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_CONSENSUS_BASE="con_base"
VCF_FILTER - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_FILTER="filter"
VCF_HETEROZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_HETEROZYGOUS="heterozygous"
VCF_HOMOZYGOUS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_HOMOZYGOUS="homozygous"
VCF_INFO - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_INFO="info"
VCF_READ_COUNTS - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_READ_COUNTS="read_count"
VCF_REFERENCE_BASE - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_REFERENCE_BASE="ref_base"
VCF_SECOND_ID - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_SECOND_ID="id"
VCF_SNV - Static variable in class com.github.seqware.queryengine.system.importers.workers.ImportConstants: Constant VCF_SNV="SNV"
VCFDumper - Class in com.github.seqware.queryengine.system.exporters: This will dump VCF files given a FeatureSet that was originally imported from a VCF file.
VCFDumper(String[]) - Constructor for class com.github.seqware.queryengine.system.exporters.VCFDumper: Constructor for VCFDumper.
VCFVariantImportWorker - Class in com.github.seqware.queryengine.system.importers.workers: Ported VCFVariantImportWorker now using our Hibernate-like entry.
VCFVariantImportWorker() - Constructor for class com.github.seqware.queryengine.system.importers.workers.VCFVariantImportWorker: Constructor for VCFVariantImportWorker.
VCFVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: VCFVariantImportWorker class.
VCFVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.VCFVariantImportWorker: Constructor for VCFVariantImportWorker.
VDOUBLE_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
VenterGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: VenterGenomeVariantImportWorker class.
VenterGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.VenterGenomeVariantImportWorker: Constructor for VenterGenomeVariantImportWorker.
verify(String, char[]) - Method in class net.sourceforge.seqware.queryengine.webservice.security.SeqWareVerifier
verifyFile(File) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: verifyFile.
verifyInput() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: verifyInput.
verifyInput() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: verifyInput.
verifyInput() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: verifyInput.
verifyOutput() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: verifyOutput.
verifyOutput() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: verifyOutput.
verifyOutput() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: verifyOutput.
verifyParameters() - Method in interface com.github.seqware.queryengine.plugins.AnalysisPluginInterface: verifyParameters.
verifyParameters() - Method in class com.github.seqware.queryengine.plugins.hbasemr.AbstractMRHBasePlugin: verifyParameters.
verifyParameters() - Method in class com.github.seqware.queryengine.plugins.inmemory.AbstractInMemoryPlugin: verifyParameters.
version - Variable in class net.sourceforge.seqware.common.module.ReturnValue
VERSION - Static variable in class net.sourceforge.seqware.pipeline.module.Module: Constant VERSION="0.7.0"
Versionable<T extends Versionable> - Interface in com.github.seqware.queryengine.model.interfaces: Interface for versioning, versions are automatically generated and iterated when a new entity is derived from a parent entity.
VersionResource - Class in net.sourceforge.seqware.queryengine.webservice.view: VersionResource class.
VersionResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.VersionResource
VFLOAT_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
VINTEGER_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
VLONG_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
VSGIDREF_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB
VSTRING_FIELD_NUMBER - Static variable in class com.github.seqware.queryengine.dto.QESupporting.TagPB

W

waitAndGetReturn(Process) - Static method in class net.sourceforge.seqware.common.util.runtools.RunTools: Wait on a process to finish, then parse information into return value
warn(Object) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.warn(Object).
warn(Object, Throwable) - Static method in class net.sourceforge.seqware.common.util.Log: See Category.warn(Object,Throwable).
watchModuleRun(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect: watchModuleRun.
watchModuleRun2(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.RedirectAspect: watchModuleRun2.
watchRunner(ProceedingJoinPoint) - Method in class net.sourceforge.seqware.pipeline.runner.LogAspect: watchRunner.
watchWorkflow(String, String) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools: This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return false.
watchWorkflow(String, String, int) - Method in class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools: This method allows you to monitor a running Pegasus workflow using a statusCmd (typically something like "pegasus-status -l dir" and, if something goes wrong, it will return a ReturnValue with exit status of ReturnValue.FAILURE, ReturnValue.PROCESSING if still running, and ReturnValue.SUCCESS if finished OK.
WatsonGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: WatsonGenomeVariantImportWorker class.
WatsonGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.WatsonGenomeVariantImportWorker: Constructor for WatsonGenomeVariantImportWorker.
wfCount(Sample) - Static method in class net.sourceforge.solexatools.util.TagUtils: Returns count of the Sample related Workflow Runs.
wfrAccession - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
wfrAncesstor - Variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.PegasusJob
WHITESPACE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageLexer: Constant WHITESPACE=25
WHITESPACE - Static variable in class com.github.seqware.queryengine.kernel.output.SeqWareQueryLanguageParser: Constant WHITESPACE=25
WIGExporter - Class in net.sourceforge.seqware.queryengine.tools.exporters: WIGExporter class.
WIGExporter() - Constructor for class net.sourceforge.seqware.queryengine.tools.exporters.WIGExporter
WORKER_CHAR_PARAM - Static variable in class com.github.seqware.queryengine.system.importers.SOFeatureImporter: Constant WORKER_CHAR_PARAM='w'
workerName - Variable in class com.github.seqware.queryengine.system.importers.workers.ImportWorker
Workflow - Class in net.sourceforge.seqware.common.model: Workflow class.
Workflow() - Constructor for class net.sourceforge.seqware.common.model.Workflow: Constructor for Workflow.
Workflow - Class in net.sourceforge.seqware.pipeline.workflow: FIXME: This Workflow object should have much of the implementation move to the common package, see WorkflowTools
Workflow(Metadata, Map<String, String>) - Constructor for class net.sourceforge.seqware.pipeline.workflow.Workflow: Constructor for Workflow.
Workflow - Class in net.sourceforge.seqware.pipeline.workflowV2.model
Workflow() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.Workflow
WORKFLOW_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant WORKFLOW_NAME="Header.WORKFLOW_NAME.getTitle()"
WORKFLOW_RUN_NAME - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant WORKFLOW_RUN_NAME="Header.WORKFLOW_RUN_NAME.getTitle()"
WORKFLOW_RUN_PREFIX - Static variable in class net.sourceforge.solexatools.util.Constant: Constant WORKFLOW_RUN_PREFIX="wfr_"
WORKFLOW_RUN_STATUS - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant WORKFLOW_RUN_STATUS="Header.WORKFLOW_RUN_STATUS.getTitle()"
WORKFLOW_RUN_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant WORKFLOW_RUN_SWA="Header.WORKFLOW_RUN_SWA.getTitle()"
WORKFLOW_SWA - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant WORKFLOW_SWA="Header.WORKFLOW_SWA.getTitle()"
WORKFLOW_VERSION - Static variable in class net.sourceforge.seqware.common.hibernate.FindAllTheFiles: Constant WORKFLOW_VERSION="Header.WORKFLOW_VERSION.getTitle()"
WorkflowAttribute - Class in net.sourceforge.seqware.common.model
WorkflowAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowAttribute
WorkflowAttributeDAO - Interface in net.sourceforge.seqware.common.dao: WorkflowAttributeDAO interface.
WorkflowAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
WorkflowAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowAttributeDAOHibernate
WorkflowClassFinder - Class in net.sourceforge.seqware.pipeline.workflowV2: WorkflowClassFinder class.
WorkflowClassFinder() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowClassFinder: Constructor for WorkflowClassFinder.
WorkflowController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowController class.
WorkflowController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController: Constructor for WorkflowController.
WorkflowController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowController: Constructor for WorkflowController.
WorkflowDAO - Interface in net.sourceforge.seqware.common.dao: WorkflowDAO interface.
WorkflowDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: WorkflowDAOHibernate class.
WorkflowDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowDAOHibernate: Constructor for WorkflowDAOHibernate.
WorkflowDataModelFactory - Class in net.sourceforge.seqware.pipeline.workflowV2: a utils class for creating the AbstractWorkflowDataModel, by reading the metadata.xml file, will load a Java based objectModel or XML based ObjectModel
WorkflowDataModelFactory(OptionSet, Map<String, String>, String[], Metadata) - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowDataModelFactory
WorkflowEngine - Interface in net.sourceforge.seqware.pipeline.workflowV2: WorkflowEngine interface.
WorkflowExecutable - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object
WorkflowExecutable() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.WorkflowExecutable
WorkflowExecutableUtils - Class in net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus: a util class to generate Java, Perl, and DirManager for dax
WorkflowExecutableUtils() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.WorkflowExecutableUtils
WorkflowIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowIDResource class.
WorkflowIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowIDResource: Constructor for WorkflowIDResource.
WorkflowInfo - Class in net.sourceforge.seqware.common.util.workflowtools: WorkflowInfo class.
WorkflowInfo() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowInfo
WorkflowLauncher - Class in net.sourceforge.seqware.pipeline.plugins
WorkflowLauncher() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher
WorkflowLauncherV2 - Class in net.sourceforge.seqware.pipeline.plugins
WorkflowLauncherV2() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowLauncherV2
WorkflowList - Class in net.sourceforge.seqware.common.model.lists: WorkflowList class.
WorkflowList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowList: Constructor for WorkflowList.
WorkflowListSetupController - Class in net.sourceforge.solexatools.webapp.controller: RegistrationSetupController This is invoked upon entry to Registration.jsp or RegistrationUpdate.jsp
WorkflowListSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowListSetupController: Constructor for WorkflowListSetupController.
WorkflowManager - Class in net.sourceforge.seqware.common.util.workflowtools: WorkflowManager class.
WorkflowManager() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowManager
WorkflowParam - Class in net.sourceforge.seqware.common.model: WorkflowParam class.
WorkflowParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParam: Constructor for WorkflowParam.
WorkflowParamController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowParamController class.
WorkflowParamController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Constructor for WorkflowParamController.
WorkflowParamController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamController: Constructor for WorkflowParamController.
WorkflowParamDAO - Interface in net.sourceforge.seqware.common.dao: WorkflowParamDAO interface.
WorkflowParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: WorkflowParamDAOHibernate class.
WorkflowParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamDAOHibernate: Constructor for WorkflowParamDAOHibernate.
WorkflowParamIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowParamIDResource class.
WorkflowParamIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamIDResource: Constructor for WorkflowParamIDResource.
WorkflowParamList - Class in net.sourceforge.seqware.common.model.lists: WorkflowParamList class.
WorkflowParamList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamList: Constructor for WorkflowParamList.
WorkflowParamListController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowParamListController class.
WorkflowParamListController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamListController: Constructor for WorkflowParamListController.
WorkflowParamResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowParamResource class.
WorkflowParamResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamResource: Constructor for WorkflowParamResource.
WorkflowParamService - Interface in net.sourceforge.seqware.common.business: WorkflowParamService interface.
WorkflowParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl: WorkflowParamServiceImpl class.
WorkflowParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamServiceImpl: Constructor for WorkflowParamServiceImpl.
WorkflowParamSetupController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowParamSetupController class.
WorkflowParamSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamSetupController: Constructor for WorkflowParamSetupController.
WorkflowParamValidator - Class in net.sourceforge.solexatools.validation: WorkflowParamValidator class.
WorkflowParamValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowParamValidator: Constructor for WorkflowParamValidator.
WorkflowParamValue - Class in net.sourceforge.seqware.common.model: WorkflowParamValue class.
WorkflowParamValue() - Constructor for class net.sourceforge.seqware.common.model.WorkflowParamValue: Constructor for WorkflowParamValue.
WorkflowParamValueController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowParamValueController class.
WorkflowParamValueController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Constructor for WorkflowParamValueController.
WorkflowParamValueController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueController: Constructor for WorkflowParamValueController.
WorkflowParamValueDAO - Interface in net.sourceforge.seqware.common.dao: WorkflowParamValueDAO interface.
WorkflowParamValueDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: WorkflowParamValueDAOHibernate class.
WorkflowParamValueDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowParamValueDAOHibernate: Constructor for WorkflowParamValueDAOHibernate.
WorkflowParamValueIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowParamValueIDResource class.
WorkflowParamValueIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueIDResource: Constructor for WorkflowParamValueIDResource.
WorkflowParamValueList - Class in net.sourceforge.seqware.common.model.lists: WorkflowParamValueList class.
WorkflowParamValueList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowParamValueList: Constructor for WorkflowParamValueList.
WorkflowParamValueResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowParamValueResource class.
WorkflowParamValueResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowParamValueResource: Constructor for WorkflowParamValueResource.
WorkflowParamValueService - Interface in net.sourceforge.seqware.common.business: WorkflowParamValueService interface.
WorkflowParamValueServiceImpl - Class in net.sourceforge.seqware.common.business.impl: WorkflowParamValueServiceImpl class.
WorkflowParamValueServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowParamValueServiceImpl: Constructor for WorkflowParamValueServiceImpl.
WorkflowParamValueSetupController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowParamValueSetupController class.
WorkflowParamValueSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowParamValueSetupController: Constructor for WorkflowParamValueSetupController.
WorkflowPlugin - Class in net.sourceforge.seqware.pipeline.plugin
WorkflowPlugin() - Constructor for class net.sourceforge.seqware.pipeline.plugin.WorkflowPlugin
WorkflowReport - Class in net.sourceforge.seqware.common.hibernate: WorkflowReport class.
WorkflowReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowReport
WorkflowReportResource - Class in net.sourceforge.seqware.webservice.resources.queries: WorkflowReportResource class.
WorkflowReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowReportResource: Constructor for WorkflowReportResource.
WorkflowResource - Class in net.sourceforge.seqware.queryengine.webservice.view: WorkflowResource class.
WorkflowResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowResource
WorkflowResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowResource class.
WorkflowResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowResource: Constructor for WorkflowResource.
WorkflowRun - Class in net.sourceforge.seqware.common.model: WorkflowRun class.
WorkflowRun() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRun: Constructor for WorkflowRun.
WorkflowRunAttribute - Class in net.sourceforge.seqware.common.model
WorkflowRunAttribute() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunAttribute
WorkflowRunAttributeDAO - Interface in net.sourceforge.seqware.common.dao: WorkflowRunAttributeDAO interface.
WorkflowRunAttributeDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate
WorkflowRunAttributeDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunAttributeDAOHibernate
WorkflowRunController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowRunController class.
WorkflowRunController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Constructor for WorkflowRunController.
WorkflowRunController(Object) - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunController: Constructor for WorkflowRunController.
WorkflowRunDAO - Interface in net.sourceforge.seqware.common.dao: WorkflowRunDAO interface.
WorkflowRunDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: WorkflowRunDAOHibernate class.
WorkflowRunDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunDAOHibernate: Constructor for WorkflowRunDAOHibernate.
WorkflowRunHtmlUtil - Class in net.sourceforge.solexatools.util: WorkflowRunHtmlUtil class.
WorkflowRunHtmlUtil() - Constructor for class net.sourceforge.solexatools.util.WorkflowRunHtmlUtil
WorkflowRunIdFilesResource - Class in net.sourceforge.seqware.webservice.resources.queries: WorkflowRunIdFilesResource class.
WorkflowRunIdFilesResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIdFilesResource: Constructor for WorkflowRunIdFilesResource.
WorkflowRunIDProcessingsResource - Class in net.sourceforge.seqware.webservice.resources.queries: WorkflowRunIDProcessingsResource class.
WorkflowRunIDProcessingsResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDProcessingsResource: Constructor for WorkflowRunIDProcessingsResource.
WorkflowRunIDResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowRunIDResource class.
WorkflowRunIDResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunIDResource: Constructor for WorkflowRunIDResource.
WorkflowRunIDsFilter - Class in net.sourceforge.seqware.webservice.resources.filters: We presume there is either a runId or a testId, not both.
WorkflowRunIDsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunIDsFilter
WorkflowRunIDWorkflowResource - Class in net.sourceforge.seqware.webservice.resources.queries: WorkflowRunIDWorkflowResource class.
WorkflowRunIDWorkflowResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunIDWorkflowResource: Constructor for WorkflowRunIDWorkflowResource.
WorkflowRunList - Class in net.sourceforge.seqware.common.model.lists: WorkflowRunList class.
WorkflowRunList() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList: Constructor for WorkflowRunList.
WorkflowRunList2 - Class in net.sourceforge.seqware.common.model.lists: WorkflowRunList2 class.
WorkflowRunList2() - Constructor for class net.sourceforge.seqware.common.model.lists.WorkflowRunList2: Constructor for WorkflowRunList2.
WorkflowRunParam - Class in net.sourceforge.seqware.common.model: WorkflowRunParam class.
WorkflowRunParam() - Constructor for class net.sourceforge.seqware.common.model.WorkflowRunParam: Constructor for WorkflowRunParam.
WorkflowRunParamDAO - Interface in net.sourceforge.seqware.common.dao: WorkflowRunParamDAO interface.
WorkflowRunParamDAOHibernate - Class in net.sourceforge.seqware.common.dao.hibernate: WorkflowRunParamDAOHibernate class.
WorkflowRunParamDAOHibernate() - Constructor for class net.sourceforge.seqware.common.dao.hibernate.WorkflowRunParamDAOHibernate: Constructor for WorkflowRunParamDAOHibernate.
WorkflowRunParamService - Interface in net.sourceforge.seqware.common.business: WorkflowRunParamService interface.
WorkflowRunParamServiceImpl - Class in net.sourceforge.seqware.common.business.impl: WorkflowRunParamServiceImpl class.
WorkflowRunParamServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunParamServiceImpl: Constructor for WorkflowRunParamServiceImpl.
WorkflowRunReport - Class in net.sourceforge.seqware.common.hibernate: Reports on workflow run metadata, returning either all workflow runs, all runs of a particular workflow, or a specific workflow run.
WorkflowRunReport() - Constructor for class net.sourceforge.seqware.common.hibernate.WorkflowRunReport
WorkflowRunReporter - Class in net.sourceforge.seqware.pipeline.plugins: WorkflowRunReporter class.
WorkflowRunReporter() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter: Constructor for WorkflowRunReporter.
WorkflowRunReportResource - Class in net.sourceforge.seqware.webservice.resources.queries: WorkflowRunReportResource class.
WorkflowRunReportResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRunReportResource: Constructor for WorkflowRunReportResource.
WorkflowRunReportRow - Class in net.sourceforge.seqware.common.hibernate.reports: Contains the workflow's Processing events, the parent Processings, the input files, the output files, the identity and library samples, as well as the total running time.
WorkflowRunReportRow() - Constructor for class net.sourceforge.seqware.common.hibernate.reports.WorkflowRunReportRow
WorkflowRunResource - Class in net.sourceforge.seqware.webservice.resources.tables: WorkflowRunResource class.
WorkflowRunResource() - Constructor for class net.sourceforge.seqware.webservice.resources.tables.WorkflowRunResource: Constructor for WorkflowRunResource.
WorkflowRunService - Interface in net.sourceforge.seqware.common.business: WorkflowRunService interface.
WorkflowRunServiceImpl - Class in net.sourceforge.seqware.common.business.impl: WorkflowRunServiceImpl class.
WorkflowRunServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowRunServiceImpl: Constructor for WorkflowRunServiceImpl.
WorkflowRunSetupController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowRunSetupController class.
WorkflowRunSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowRunSetupController
WorkflowRunsFilter - Class in net.sourceforge.seqware.webservice.resources.filters: We presume there is either a runId or a testId, not both.
WorkflowRunsFilter() - Constructor for class net.sourceforge.seqware.webservice.resources.filters.WorkflowRunsFilter
WorkflowRunStatusResource - Class in net.sourceforge.seqware.queryengine.webservice.view: WorkflowRunStatusResource class.
WorkflowRunStatusResource() - Constructor for class net.sourceforge.seqware.queryengine.webservice.view.WorkflowRunStatusResource
WorkflowRuntimeResource - Class in net.sourceforge.seqware.webservice.resources.queries: WorkflowRuntimeResource class.
WorkflowRuntimeResource(Context) - Constructor for class net.sourceforge.seqware.webservice.resources.queries.WorkflowRuntimeResource: Constructor for WorkflowRuntimeResource.
WorkflowService - Interface in net.sourceforge.seqware.common.business: WorkflowService interface.
workflowService - Variable in class net.sourceforge.solexatools.webapp.controller.ManageWorkflowsController
WorkflowServiceImpl - Class in net.sourceforge.seqware.common.business.impl: WorkflowServiceImpl class.
WorkflowServiceImpl() - Constructor for class net.sourceforge.seqware.common.business.impl.WorkflowServiceImpl: Constructor for WorkflowServiceImpl.
WorkflowSetupController - Class in net.sourceforge.solexatools.webapp.controller: WorkflowSetupController class.
WorkflowSetupController() - Constructor for class net.sourceforge.solexatools.webapp.controller.WorkflowSetupController: Constructor for WorkflowSetupController.
WorkflowStatusChecker - Class in net.sourceforge.seqware.pipeline.plugins: This plugin lets you monitor the status of running workflows and updates the metadata object with their status.
WorkflowStatusChecker() - Constructor for class net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker: Constructor for WorkflowStatusChecker.
WorkflowTools - Class in net.sourceforge.seqware.common.util.workflowtools: This class provides methods for dealing with Pegasus workflow log directories for example watching a directory to detect when a workflow has failed or finished.
WorkflowTools() - Constructor for class net.sourceforge.seqware.common.util.workflowtools.WorkflowTools
workflowTools - Variable in class net.sourceforge.seqware.pipeline.workflow.BasicWorkflow
WorkflowValidator - Class in net.sourceforge.solexatools.validation: WorkflowValidator class.
WorkflowValidator() - Constructor for class net.sourceforge.solexatools.validation.WorkflowValidator: Constructor for WorkflowValidator.
WorkflowXmlParser - Class in net.sourceforge.seqware.pipeline.workflowV2
WorkflowXmlParser() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.WorkflowXmlParser
wrapup() - Method in class net.sourceforge.seqware.pipeline.workflowV2.AbstractWorkflowDataModel: to be Overridden by the workflow author
write(Kryo, Output) - Method in class com.github.seqware.queryengine.util.FSGID
write(Kryo, Output) - Method in class com.github.seqware.queryengine.util.SGID
writeKeyValueFile(File, Map<String, String>) - Static method in class com.github.seqware.queryengine.system.Utility: Write to output file a tab separated key value file represented by map
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
writeReplace() - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.AtomPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.FeatureAtomPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.FSGIDPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.SGIDPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QESupporting.TagPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ACLPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.AnalysisSetPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureListPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeaturePB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.FeatureSetPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.GroupPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.MoleculePB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferencePB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.ReferenceSetPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.TagSetPB
writeTo(CodedOutputStream) - Method in class com.github.seqware.queryengine.dto.QueryEngine.UserPB
WS_PASS - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
WS_URL - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys
WS_USER - Static variable in interface net.sourceforge.seqware.pipeline.runner.Runner.Keys

X

XmlizeFileSet - Class in net.sourceforge.seqware.common.model.adapters: XmlizeFileSet class.
XmlizeFileSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeFileSet
XmlizeIUSSortedSet - Class in net.sourceforge.seqware.common.model.adapters: XmlizeIUSSortedSet class.
XmlizeIUSSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeIUSSortedSet
XmlizeLaneSortedSet - Class in net.sourceforge.seqware.common.model.adapters: XmlizeLaneSortedSet class.
XmlizeLaneSortedSet() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeLaneSortedSet
XmlizeXML - Class in net.sourceforge.seqware.common.model.adapters: XmlizeXML class.
XmlizeXML() - Constructor for class net.sourceforge.seqware.common.model.adapters.XmlizeXML
XmlTools - Class in net.sourceforge.seqware.common.util.xmltools: XmlTools class.
XmlTools() - Constructor for class net.sourceforge.seqware.common.util.xmltools.XmlTools
XmlWorkflowDataModel - Class in net.sourceforge.seqware.pipeline.workflowV2.model
XmlWorkflowDataModel() - Constructor for class net.sourceforge.seqware.pipeline.workflowV2.model.XmlWorkflowDataModel
xreflink - Variable in class net.sourceforge.seqware.queryengine.webservice.model.AnalysisType.ANALYSISLINKS.ANALYSISLINK
XSI - Static variable in class net.sourceforge.seqware.pipeline.workflowV2.engine.pegasus.object.Adag

Y

YanHuangGenomeVariantImportWorker - Class in net.sourceforge.seqware.queryengine.tools.importers.workers: YanHuangGenomeVariantImportWorker class.
YanHuangGenomeVariantImportWorker() - Constructor for class net.sourceforge.seqware.queryengine.tools.importers.workers.YanHuangGenomeVariantImportWorker: Constructor for YanHuangGenomeVariantImportWorker.

Z

Zip - Class in net.sourceforge.seqware.pipeline.tools: Zip class.
Zip() - Constructor for class net.sourceforge.seqware.pipeline.tools.Zip
zipDirectoryRecursive(File, File, String, boolean, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: zipDirectoryRecursive.
zipDirectoryRecursiveOld(File, File, String, boolean, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: zipDirectoryRecursiveOld.
ZipFileUtil - Class in net.sourceforge.solexatools.util: ZipFileUtil class.
ZipFileUtil() - Constructor for class net.sourceforge.solexatools.util.ZipFileUtil
zipListFileRecursiveOld(List<File>, File, String, String, boolean) - Static method in class net.sourceforge.seqware.common.util.filetools.FileTools: zipListFileRecursiveOld.
zygosity - Variable in class net.sourceforge.seqware.queryengine.backend.model.Variant

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